KX engine in a zilla frame == lots of vibrations. I don't think the KX500 is a counter balanced engine. I think the best bet is to figure out the bugs with the Zilla engine and you should love it. I know what you mean about expecting a lean run away rev, but it didn't happen. The issue with the Lectron was the fuel input into the bowl. That was the restrictive area of my setup. It would run great until I went to 4th or 5th gear and tried to go Wide Open. That is when it would fall on its face (like I hit the off switch). Shut off the throttle for a second and then it would be running again as expected (at least until you try W.O. again).
Sounds like you have a full build with all your mods. I still think your running into an issue with the Lectron, as that was my exact problem with mine. Was a new Lectron setup by Packard also with everything you had (except for the larger bowl).
Stay with it... you have a lot of $$$ and time spent on your quad and I think you are close to getting thru the last issue.
P.S. With my build (similiar to yours above) my TM38 (modified by HPR) liked the 640 main jet when dyno tuning!