Mods below...running a 100 shot with MSD window switch. I shift right around 6000-6200, limiter is set for 6500 rpm. Where should my window be?

 

A couple hundred rpms below where you shift

 

I'd put it a few hundred rpm's below your rev limiter.... As long as you're not keepin it floored while you shift, you're nitrous is going to quit spraying when you shift anyways..... (If you're using a wide open throttle switch).

I run an automatic, and I've been sprayin through the shifts on a big shot for a year on my current tranny.