Weird throttle issue?

I ride a 1979 kz400 ltd and I gots a weird throttle issue. After warmed up and ridden for quite a bit (30 minutes continuously), my bike develops something that I don't know if I would call it a hesitation or a bog. Anyways, what happens is after said conditions above, my bike when I let go of the throttle completely for whatever reason (downhill, slowing, etc.) and then I get back onto the throttle to cruise, it will sound raspy and feel like it is starving for fuel, that is UNTIL I give the throttle an extra blip (over half throttle) and return to cruise throttle position, then the bike will behave normally.

It has done this for a couple months before winter but did not have this issue when I bought the bike almost two years ago. Aside from this issue, this bike is perfect. Runs perfect and drives perfect.

Things i have done to try and fix this:

1) cleaned the carburetors. I have done this Several times in the last couple months trying to fix. Not that they were dirty, but I was fiddling with the carbs off the bike so I figured might as well clean them while I was at it.
2) put an intake gasket between the boot and the engine. I was taking the boots off to inspect for cracks and wanted to replace the screws with allen head bolts while I was at it and figured it wouldn't hurt to put a gasket there.
3) checked for vacuum leaks with wd40, carb cleaner, and propane. I do not have any sort of vacuum leak around the intake system.
4) bench synced the carbs. This is self-explanatory.
5) checked the fuel mixture screws were out 2.5 turns (didn't have to change them).

I do want to mention that my headers are mismatched colors. Cylinder one is yellow (lean) and the second is blue (rich), I'm not sure if this is left over from when I bought the bike (carbs were horribly out of tune making cylinder one run incredibly lean) or if the first cylinder is continuing to run lean. I did do a plug chop and they both plugs had normal wear. Is this carb related or could this be a partially sticking timing advancer? I put this is carburetors because it's a throttle related complaint.

Does the bike have the stock air box and filter? Have you made any changes there since buying the bike? Ed