Bodi: Thanks for the feedback on the slide needles. I figured as much seeing how there really isn't any way to stop them from moving. Wanted to make sure.
Hondaman: I originally decided to use the old boots, did the wintergreen thing which softened them up nice, and replaced the o-rings. Once I started having all these issues I decided to just buy new ones. Sirius had them in stock. No difference. The coils are new and I have not tested them. Definitely something to look at.
So with the needle in the 4th groove, Keihin 80 mains and 38 pilots, floats set at 23mm and everything perfectly synched, the bike ran like an absolute bag of crap. From idle to 1/4 was a lot of hesitation and sputtering, 1/4 back down to idle in gear it would just quit. 1/4 to 1/2 was sluggish and more hesitation, 1/2 to 3/4 was a little better, but 3/4 to WOT seemed to be a lot better. Actually hit 9500rpm in 4th and pulled decently.
So this is the perfect example of why you only change one thing at a time, because now I'm going to have to go back and figure out which of the 3 changes I made has had a negative effect. At least I'm now fairly certain that the 80 main is right. Won't know for sure until the plug chop.
nvr2old: I've decided to stop annoying my neighbours (and myself) and replace the megaphone exhaust with original. It's arriving tonight. I'm hoping it also alleviates some of these tuning issues.
So the weekend plan (with the wife and kids out of town until Monday

) is to install the stock exhaust and start doing plug chops. Beer intake levels will be directly proportional to success levels. Success>Beer.