IMHO...
Fist if this is to be a race bike, pull the rear shock and replace it with an alum strut. In shaft bikes I raced in the past, I used a strut length that gave me a horzonal shaft. I know most people drop the rear way down but because a shaft bike tries to "climb the gear", I always felt it was best to put that power down. May not make any difference but one always has opinions. building for E85 is the way to go, but you really have to pull the heads to make that work for you. The reason E85 is so good is that it lets you run more compression and more advance. If you build an E85 engine with stock compression you are not really getting any real boost.
I know Sean did some work looking at the the cams and pistons and I think he said there was not much room for much bigger cams. You deck the block and cut the head and you have even less. If I were building a drag bike out of the gen 2, that engine would be up on the bench and I would being doing a lot of measuring and testing with modeling clay to get the valve pockets cut right and hopefully get a bit more cam. Of course bumping the compression and extending the valve timing is what you DON'T want to do if you put a blower on it.
Tuning pipes is a matter of length and size, and length of megaphone. Its really had to do for a V4. Most pre made pipes are made to function over a wide RPM range. You only need a lot of performance over a very short RPM range in a drag bike. The old school experimenter in me says I might try making up a 4 pipe setup and spend some time on the dyno. "ram tuning" is all about timing when certain presser waves arrive at the valve. But that means nothing if you supercharge it.
I guess what I'm saying is you should build a normally aspired motor OR an supercharged motor. Building us an e85 normally aspired motor then just dropping a supercharger on it is NOT a good way to go. I would go with NO2 OR supercharging. It really makes a difference in the way you should build your motor.
But then I'm just a real old racer and don't know anything about all these fancy new things...
Craig