Stutter when accelerating hard 5000-8000 rpm range

[Gnasher]

As for being Ivanized or jetted. I'm not sure.

Just pull off a carb top and check if the springs been cut to shorten it, it will be blatantly obvious.

After some more testing it appears it's only doing it in second gear....so now i'm actually guessing 2nd gear broke a tooth or something.

If second gear had failed you know about it all the time, not just while accelerating and it wouldn't go away.  From what you said, your problem is either fuel/air mixture, an air leak and or fueling is leaning off/being restricted or it's high tension circuit i.e. coil/lead/plug breaking down or leaking.  Changing the end can will not cause this, just bolting on any end can will have little effect to top end power. 

You keep mentioning pushing it to the limit, pushing a FZS1000 to the limit in second is probably why you had an 80mph off, if nothing else mate slow down or the bike possibly you are likely not to last very long on the road.