Dude. Pics. We are just wasting time here until we SEE why your set up is failing to work.
You ARE just wasting time. From the beginning he's been set on making the Kehins work and providing an option to stock carbs. Not an entirely bad idea in the realm of cost and availability, but that whole point has been ignored in "defense" of properly set up stockers. Not every rider/builder/enthusiast is a purist. OP isn't interested in making the stockers work, he already doesn't like them. I've never been big on CV carbs on modified (and that includes pipes and pods) bikes either. They're just too sensitive to the small changes, which eclipses any real gains.
That being said, the motor is an air pump of a given displacement. The only thing that makes it sensitive to changes in exhaust or filters is the carb itself and it's ability to feed the motor the proper air fuel mix. Touchy carbs are touchy carbs. If minor changes require such fine tuning just to run, why not use something that makes the job easier and cheaper? Unless you're doing a resto, it shouldn't really matter.
I rode a stock XS400 home from purchase and it ran like a raped ape. Now I can't get it to stay lit. NOTHING changed. It just sat for a week or so. And I'm not worried about it until I need to be. It's a back burner project at this point, so not seeking advice at the moment.
Good diagnosis thread, and all info is worth reading and learning.
To the OP, XS650 boots will not work on XS400 intake, the port center is .060" off the centerline between the bolts, and the port size is bigger on the 650, and the bolt spacing is different... I just got done machining intake flanges for both motors (for single carb manifolds) and they both fit what they're supposed to fit, but not each other.
With a .005-.008 valve lash you are out of spec.
