My ZZR1100 was running rough and when I checked the valve clearances there were six tight on the exhaust side. I also balanced the carbs, and it’s now much smoother and responsive, but it sort of misses or stutters between two and four thousand revs
If it was OK just before you did all this work, check that all the hoses that were connected to the airbox are back as they should be. It could be a weak mixture on the pilot circuit and it may need the carbs stripping down and cleaning out thoroughly. Before you go there try super unleaded with Redex to see if it’s any better.