Andy, I know this seems like an obvious question, but what are the differences in set-up between your bike and your wife's? Have you tried copying her set-up?
I am starting to think her bike is a freak.
It has a stock carb. (the modded one wouldn't idle- my fault) A modded intake manifold that doesn't match the carb side now. A KN varaitor and roller weights. I cant even remember what weights it runs. It even has stock exhaust. We have the same belt. I remember when we got her bike I gave her the KN varaitor cause I was near maxing it out and couldn't get any speed. (stole the Malossi off this bike)
My bike runs the same jets, same intake and filter. Only major differences are tires- boppers on stock rims and a 6" stretch and the fact she is at least 50-60lbs lighter than me.
Just a thought, but with that fairly-fresh blue Polini contra, 4.5s may not be heavy enough to force the clutch completely open.
The engagement springs shouldn't affect anything except
what rpm the clutch engages. Shouldn't have any effect on top speed.
Still running a Gates belt? If you have a stock Bando laying around, give it a try and see how it affects the top speed. Just to satisfy an old man's curiosity.
You are right i should be running heavier weights. I am going to swap the 6.1g Polini rollers tonight and see if they're any better.