Thunder Manufacturing Hyper Charger
I was always intrigued by the looks of a Hyper Charger but had read many horror stories about their setup and tuning.  The thought of spending the money for a Hyper Charger and having the bike not idling or even running properly, was enough to keep me more than satisfied with the RAK modification.  I had decided that I would dress up the RAKed stock air box with some type of a cover or insert.  After all, the RAK cost less than $10, is an excellent modification and the performance gain was outstanding.
Then I started corresponding with a guy who had a VStar 650 Custom, had installed a Hyper Charger and was thrilled with its performance.  So naturally, I began to ask questions.  As it turns out, this guy is a lot smarter than I am when it comes to performance mods, engines and carburetors.   He used to drag race motorcycles and cars so he knew how to tweak, tune and set up all the high tech gizmos, like the Hyper Charger.  PLUS,... he had already done all the tuning leg work and had it running great!  What could I do?  I had to get one of course!
The Thunder Manufacturing  Hyper Charger with the standard cover plate and butterflies.  It's a very nice piece of equipment!
The guy I'm referring to is Jeff Sweigart and all the setup and tuning details on this page are a result of his efforts.  He's helped a lot of people install and set up their Hyper Chargers,...including me.  In fact, with his help, I re-jetted the carbs to his specifications, installed the Hyper Charger, started the bike and drove away!  How much easier does it get?!  By the time Jeff got to me, he had developed the setup and tuning into pretty much of a  "cook book" approach for the 650s.  The following write up is basically what I learned from Jeff.
One word of caution!  Jeff has informed me that the Hyper Charger may not work with an unmodified stock exhaust system.  Either after market pipes should have been installed or the stock exhaust system should be modified to make it a more free flowing system.  I'm running the semi-gutted slash cut stock pipes that are described in a separate page on this site.  
Most of the pictures below have links to pop ups with larger pictures for more detail.  Just click on the picture to open the popup and close it when you're done, to continue.
The Thunder Manufacturing order consisted of a Kuryakyn Hyper Charger, the Thunder Hyper Charger adapter for the VStar 650 and their Dynojet stage 3 jet kit also for the 650.  I placed the order on a Thursday and it was on my doorstep the following Tuesday.
The first thing I did was to open all the boxes to inspect everything and familiarize myself with all the parts.  Having done that, I started to disassemble the bike.  I first removed the speedometer housing and the gas tank.  I removed the stock air cleaner housing and the duct that goes into the air box on top of the carbs.  The lower bracket that is used to mount the air cleaner housing and the carb vent hose was also removed.  The carb vent hose was left to hang under the carbs.  I admit, it's kind of unsightly and I'll have to do something with it later.  The clamps that hold the air box to the carbs and the down duct to the air box were loosened.  You have to fiddle with it but these two pieces will come apart and off the bike.  Now, I was ready to begin the business of re-jetting and installing the Hyper Charger. 
The miscellaneous hardware, jets and needles that are needed to re-jet the carburetors and install the Hyper Charger.
I set out all the hardware parts that I was going to use.  A pair of 128 jets, needles set with the clips on the fifth groove, two spacer washers, a "T" fitting and rubber hose, adapter gasket, drill bit and metal screw to remove the idle mixture plugs and 7, 6mm screws for mounting.  The jet kit came with 4 sets of main jets; 120s, 124s, 126s and 128s.  The instructions suggest using 124 jets and set the needles on the 4th groove.  Jeff recommended the 128s and the 5th groove for the needles.  I went with Jeff's recommendation.
I had previously removed the AIS so I used the "T" to tie both intake manifolds together and then used the rubber hose that was included with the kit to connect the "T" fitting to the Hyper Charger.  In the stock configuration, the front intake manifold tube is used to drive the AIS.  The rear intake manifold is plugged off with a short hose and a plug.  I replaced the short rear intake hose with a piece of hose about 5 inches long.
The parts that are needed to assemble the adapter and get it ready to install on the bike.  The ring gasket must be removed from the back of the stock air cleaner housing.
The ring gasket on the stock air cleaner housing is glued in place.  A little gentle persuasion and it was removed.  I cleaned the glue off the ring gasket with some Goo-Gone.  In the picture above is the stock up duct that was removed from the air cleaner housing.  I had previously covered it with a piece of chrome rocker panel tape from Pep Boys.  I also shortened the drain hose that is attached to the bottom of the up duct.  I shortened it to about 2" to keep it hidden behind the Hyper Charger.  The two black brackets are used to attach the adapter to the stock air cleaner mounts that are attached to the front and rear cylinder heads.
The ring gasket from the stock air box mounted to the back side of the Hyper Charger adapter.
The adapter assembly is temporarily mounted to the stock up duct.
The ring gasket has a groove in it that fits over a lip on the back side of the Hyper Charger adapter.  There's no need to glue it in place like the stock assembly.  The fit is excellent so there is no leakage and it certainly isn't going anywhere.
Next comes the re-jetting required for the installation.  I started with the needle replacements on the right side of the bike.
This shows a view from the top of the carbs looking down into the venturis.  You can see the vacuum slides and needles.  The tapered end of the needles fit into the needle jets in the wall of the carbs.
This shows a view of the right side of the carbs with the covers on.  The clamp for the choke slide has already been removed and the choke cable is hanging free.
The covers have been removed and the vacuum slide assemblies with the slide springs are exposed.
The slide assemblies have been removed.  The needle jets can be seen protruding from the carb wall on the inside of the venturis. 
The pictures above, show a couple of views of the right side of the carburetors.
The yellow arrow in the picture above points to the wire harness for the carb heaters.  I disconnected the wire harness at the connector located under the seat and moved the wires out of the way for easier access to the carb covers.  The red arrows point to the idle mixture screws.  I had already re-jetted the carbs previously for the RAK mod so the brass plugs had already been removed.  Included in the jet kit are a drill bit and self tapping screw to remove the brass plugs.  The idle mixture screws are recessed about 1/4".  The drill bit is used to drill a pilot hole for the sheet metal screw through the top of the brass plug.  You have to be careful to not let the bit penetrate too far and damage the idle mixture screw under the plug.  Once the hole is drilled, the screw is threaded a few turns into the plug and a pair of pliers can be used to pull the plug from the carb body.  The idle mixture screws should be turned in (clockwise) until they seat gently.  Open each idle mixture screw 3 1/2 turns (counter clockwise).
The pictures below show the idle mixture plug and screw from an 1100 carb, but the process of removing the plug is the same for the 650.
The pilot hole has been drilled in the plug.  Note that the hole is just beginning to break through the plug, not drilled through the plug.  You don't want to damage the idle mixture screw under the plug.
The self tapping screw has been threaded into the pilot hole that has been drilled in the plug.  Use pliers to wiggle the screw and pull the plug out. 
As I mentioned, I had already re-jetted once, so the brass carb cover screws had been replaced with steel allen head bolts.  The allen head bolts are a breeze to remove.  The stock brass screws are very soft and can be a real chore, as the heads strip easily.  Some have used a posi-drive bit very successfully to remove the brass screws.  I originally removed the carbs from the bike to work on the screws.  Some of the heads stripped as expected and I ended up cutting a single deep slot in the heads of the screws and using a large flat blade screw driver to remove them.  Whatever you do, replace those blasted brass screws with allen head bolts!  Stainless allen head bolts are the best but I couldn't find any at the time so I used plain steel.  As you can see from the pictures, they rusted in no time at all.  It doesn't hurt anything but they look like crap.  I've got to get stainless!!
Once you carefully remove the cover plates, the vacuum slides are exposed with the slide springs.  Remove the springs and carefully remove the slides by gently pulling on the diaphragm edges. 
Another look down into the venturis with the slides and needles removed.  The arrows point to the needle jets located on the venturi walls.
The vacuum slide and needle assemblies ready to be worked on.
The vacuum slide assembly parts.  The slide, needle with black spacer/seat, clip on the 5th groove, spacer washer, needle seat spring and needle cap.
To disassemble the needle from the slide, remove the needle cap with a screw driver.  Be sure to hold the vacuum slide by the plastic cylinder body and not the diaphragm.  Handle the diaphragm as little as possible to avoid ripping or damaging it.  Once the needle cap is removed, the needle and needle seat spring will fall out of the slide.  Note the little nub on the black nylon spacer/seat, indicated by the red arrow in the picture above.  This nub MUST fit in the tiny hole in the base of the vacuum slide when it's reassembled.   In the picture above, the red arrows point out the needle jets on the venturi walls.  The needle jets on my carbs stick out from the venturi walls about 1/16".  On some carburetors, the jets may be flush with the venturi walls.  Take the new needle and install the new circlip in the 5th groove if the jets protrude out from the venturi walls.  Install the clips in the 4th groove if the needle jets are flush with the walls of the venturi.  Remove the black spacer/seat from the old needle and push it onto the new needle, up against the circlip.  A spacer washer is included in the jet kit.  Place the spacer washer on the top of the needle against the circlip.  Place the needle seat spring on the top of the needle and insert the new assembly into the slide making sure the nub seats in the tiny hole in the base of the slide.  Install the needle cap and tighten it firmly but not excessively.  Make sure it's not cross threaded or over tightened!
Insert the slide assemblies back into the carbs being careful to align the diaphragms in their seats.  Gently move the slides in and out a short distance to make sure that they are free moving.  Place the springs back in the slides and put the covers back on.  Remember, yourself a favor and replace those brass screws with 8, 4mm x 10mm allen heads,... stainless if you can get them!  The bottom right hand screw on the rear carb is just in front of the choke slide.  You may have to put a couple of washers on that bolt before installing it in the cover plate to keep the choke slide from binding on the shaft of the bolt.  A 10mm bolt here, is a little long but it will work fine with a couple of washers.  Reattach the carb heater wire harness and put the bracket back on the choke cable end.  The needles are done!
Well, on to the jets!
The main jets are housed in the float bowls on the left side of the carbs.  The idle speed adjustment knob/cable will have to be moved out of the way to get to the cover screws.
The float bowls house the main jets, pilot jets and floats.  The carb vent hose is seen between the two carbs and is routed down through the heat shield between the cylinder jugs.
Remove the covers here, just like the other side.  The only difference here is that gas in the float bowls will drain out onto your bike.  Be ready with a couple of rags to catch the gas as it leaks from the float bowls.  Keep track of the placement of all the brackets and holders.
Once the covers are removed, you'll be able to see the main jets, indicated by the red arrows in the picture above.  The main jet on each carb is located between the floats.  Be careful not to hit the floats or bend the float adjustment tang.  It can be a real bear getting the floats adjusted again if they become misaligned.  The yellow arrow points out the carb vent hose.  Make sure the vent hose remains intact and is not bent or kinked.
The main jet standoffs end in a hex head fitting that can be held with a small wrench while a screw driver is used to remove the jets.  Install the new 128 jets.  Replace the covers.  Again, use the allen heads.  Use 8, 4mm x 12mm bolts for these covers.  Attach the idle speed adjustment to its bracket.  Jets are done!
Now to attach the Hyper Charger.
The back side of the Hyper Charger.
Connect the "T" to the intake manifold hoses as described earlier.  The vacuum hose included in the kit is used to go from the "T" to the Hyper Charger.  The yellow arrow in the picture above points to the vacuum chamber inlet on the backside of the Hyper Charger.  After mounting the Hyper Charger to the bike, attach the vacuum hose to this inlet.
The red arrow points to the butterfly adjustment screw.  This screw determines the travel endpoints of the butterflies.  This screw needs to be shortened or replaced with a slightly shorter screw.  If left the original length, it will hit the cylinder fins on the front cylinder.  The screw has to be shortened and the lock washer removed.   If you gently hold the butterflies all the way closed and turn the screw in, you will feel it hit the butterfly push rod and the butterflies will start to be forced open.  The length of the screw needs to be adjusted so that when the screw is fully turned down and seated the butterflies are open about 1/8" past the fully closed position.  Cutting about 1/4" off the end of the screw should do it but a bit of trial and error fitting is recommended.
Mount the supplied gasket to the Hyper Charger adapter.
Here, the adapter and the up duct are being trial fitted to the bike.
The left adapter bracket attached to the rear cylinder air cleaner mount.
The right adapter bracket attached to the front cylinder air cleaner mount.
As you trial fit the adapter and mounting brackets to the bike, leave all the bolts and band clamps slightly loose.  Don't tighten them down yet.  Once the Hyper Charger is mounted to the adapter, you'll have to rotate and shift the entire assembly around a bit to make sure that it is on straight.  Also make sure that the Hyper Charger and adapter are not bumping or rubbing against any of the engine surfaces.
Once you're satisfied with the fitment, tighten the band clamp where the up duct fits into the air box duct on top of the carbs.  Next, tighten the band clamp on the ring gasket attached to the adapter.  Remove the Hyper Charger and fully tighten all the band clamps and the bracket bolts.  Mount the Hyper Charger again to the adapter and install the mounting bolts with medium strength LockTite.  Don't forget the LockTite!  The last thing you want is for one of these bolts to vibrate loose and be ingested into your motor.
Reinstall the gas tank and speedo assembly.  Reattach all the fuel lines, put the seat back on, start her up and go for a ride!
Enjoy your new toy!
It's done!