Bike hesitates at around 6000 RPM

Sorry for all the posts lately, I am just really trying to get this GPz550 off my hands.

I fixed the spark plug wire on cylinder 2 so it no longer arcs across the cooling fins.
I removed the vacuum operated emissions switch, plugged the reed cases with vinyl plugs from the hardware store, plugged the vacuum nipples on the carbs with vinyl plugs, set the float heights so they are all within spec (on the lower end, however) per the clear tube test, and bench synced the carbs. There are no air leaks to speak of.

The bike starts quick (without the choke even) and idles easily. In first gear though, I can only get up to ~30mph. The bike gets to 6000rpm and hesitates a bit and stutters through to 7500/8000rpm without accelerating. The issue gets a little bit better in second and third gears, but it still feels like a bit of a dead zone.

The bike does have pod filters and I don't remember it acting this way prior to the spark plug issue. My guess is that it's running lean at that speed? I think that would be the main jet, right? If the floats are on the lower end (about 2-3mm below gasket), could adjusting them help? To reiterate, the bike has run with pods and this jet set up for years. I'm still a little iffy on if float height can cause a lean condition at high engine speeds.

Thanks for all your help lately!

A simple way to identify, as a starting point, if it is running lean: Tape closed a portion of the pod filters and test ride it. This, in effect, richens the mixture and will permit you to discern an improvement or deterioration of performace, at above (at least) half throttle. I suggest taping (¾inch wide electical tape) the small end of the pods...
If performance improves then you will know it is running lean!
This will indicate that you should first focus you attention on fuel/air, then possibly the following:
weak / intermittent spark.
stuck mechanical spark advance mech.
low compression.

I just had a very similar issue with my 750. In the end it was due to me running resistor plugs with resistor caps - oops! After I switched plugs it almost disappeared. The last bit of hesitation around 6500 rpm was due to a stuck vacuum piston in carb #2. It's running fine now - not absolutely perfect, but almost. I think I either need to up the main jet size or shim the needle (top end is great which is why I think the jet is OK). I have Keihin CV carbs, not sure what you have so the carb stuff may not help...

Another trick a carb specialist told me about is "when it starts to break up lift the choke lever and see if it gets better"
That would point towards lean main jets.
He also said be careful doing it.