During Rebuild did you vacuum test the Air Cut Valve's (p/n 16510-MAL-600)? During my recent rebuild I had the same symptoms as yours and discovered one of these valves had failed. Interestingly enough, the propane test did not reveal this issue as the failure is internal to the air-flow chambers within the carb.

I didn't, and I suppose it could be the tubing or the valve itself? I don't suppose there's a test for that while it's on the bike that anyone knows about huh? I do get quite a bit of popping upon deceleration but put that down to the missing reed valves (recently desmogged) and the pilots needing adjusting.
I think I'll try the following in this order (easiest first):
1. recheck for vacuum leaks with carb cleaner
2. test cylinder compression
3. pull the carbs and check the air cutoff valves.