Tuning out the 5Kto 6k stutter

My post on possible intake reversion problem got so long I decided to start another thread to report some findings. My bike:
79 KZ1000
1075 kit with 10:1 cr
V&H 4 into 1 pipe
Also tried a 4 into 1 pipe that was longer from the 80's (Kerker maybe?)
K410 cams set at 108* lobe separation
Minuni BS34 carbs hooked to the factory airbox, K&N filter.
Head had only 4K miles, so I just lapped the stock valves.
Head was ported by an amateur-me. The runners taper from 34MM to 29mm and are equal volumes.
Timing is factory specs and the advance works.
Spark looks slightly weak, voltage at the coils is 11.5V.

Problem was a 5-6K stutter only when accelerating at WOT, not partial throttle. I was able to get the jetting real good and through high velocity porting get the stutter 99% gone. Only one nanosecond "miss" at 5K with WOT. Playing around yesterday I took the exhaust baffle out and got interesting results. Go WOT (no baffle) at 2K rpm in high gear and it spits and sputters to 4K then pulls clean to 11k with a much stronger top end, and zero stutter 4-11K. With the baffle go WOT at 2K and it pulls strong all the way to 11K with only the one extremely slight miss at 5K, but the top end is weaker than with open pipe. Just goes to show everything has to operate together as a complete system.