What is the elevation of the track you race at? Edit -- never mind I looked it up its at 925 feet. East coast air this time of year is supposed to be killer.
So, do you squeeze out of the hole or not? I still don't see a clear answer on that. That is important, because if you don't, the 28 tall tire could be a factor vs a 26. But if you squeeze out of the hole, then I don't believe the 28 is a factor. It would most definitely be a factor N/A, however.
Check your plugs, as stated. What is your total timing at WOT? How do you know the car is "properly tuned"? Obviously something is wrong because as you point out yourself, it should be faster/quicker with the 100 shot. Exactly where did you install your cams at (advanced/0/retarded).