Start out with the small checks such as air induction and fuel flow. Make sure all cylinders are firing. Then get your carbs checked out. Also how are you riding the bike? Are you using each gear to its full potential? If you put it in 5TH and think you are going to hit a hundred anytime soon think again.

 

This may be a bit out of left field, but could it be that your rev limiter is kicking in, in the wrong rev range.........
What revs are you doing at 100MPH ?
My CBR1000F is only doing 6100RPM at 100MPH, and the rev limiter cuts in at around 10800RPM.

It could also be fuel starvation, as has been mentioned above.
Maybe the mapping for the injectors is out, or even your ECU is starting to fail ?
I've seen all of these symptoms before, and there are so many answers.
Pity we can't hear the bike..................

 

Yeah you need to find out what the correlation of conditions is for the power loss. How many R's and what gear? If you have room to, shift up or down a gear, see what it does. I've never heard of factory speed governing nor have I heard of someone retrofitting their own, so I wouldn't consider that.