I need some help with this matter of the bike stuttering? New intake boots and seals! Very very clean carbs! Also all new seals! No leaks? I'm running filter pods and stage 3 jet kit with 4 into 1 headers
Did you change your gasoline? I had a bike that sat for a couple years and I drained out approximately 2.5 gallons out of my 3 gallon tank. The bike ran like crap. I did a more thorough job of draining the tank and it was a night and day difference.
Assuming the bike is rideable, mark the edge of the twist grip flange with a spot of white out and put matching spots on the twist grip house at closed, 1/4 open, 1/2, 3/4, and wide open. Then ride the bike and see where it runs badly. As a general rule below 1/4 throttle is the pilot jet circuit, the cutaway affects around the 1/4 throttle mark. The needle jet is 1/4 to 3/4 throttle, and the main jet is dominant above 3/4 throttle.
You probably have cv carbs so you can't directly control the slides, but if you hold it at a given throttle setting the slide should match the butterfly after it stops accelerating. Probably holding over 1/2 throttle on a gsxr 1100 is dangerous for you and your license.
If it runs bad at a particular rpm but not at a particular throttle setting it's probably electrical and not carbs.