Sorry I can't offer an answer, but I have to say my bike has suffered a similar fate after getting it back from the shop last Friday. I too had intermittent problems with fuel delivery, and last week they became permanent.
Turned out my carbs had rust and other junk and the shop cleaned them out. The first day I got it back it ran great. The next day it started stalling at idle.
We put fuel line cleaner fluid in it as a stopgap measure until I brought it back after the Labor Day weekend. That appeared to work intermittently, but not much came out of that. As the weekend progressed the situation got worse. I got home from a day's ride and when I went back that evening to ride out, I couldn't start the bike.
I have big long hill by my apartment and took the bike down it to bump it. After a couple of bumps I finally got it going. Unfortunately I was paying so much attention to this issue that I didn't realize how much speed I had gained from keeping the engine rev'd up, turned at the bottom a bit too fast and wiped out. Annoyingly the engine was still running with the bike on it's side!
This morning I limped the bike to the shop and had to bump it down that same hill again. This time I was almost at the bottom before that damnned engine finally fired up. I was getting pretty nevous.
I don't understand this strange symptom, and it's surprising to me that you appear to be suffereng the same fate after a carb cleaning (and in your case, a rebuild). That doesn't hold too much promise for the situation with my bike.
I'm one step removed from junking my '400. If the repair bill from the wipeout is high enough, that's exactly what I'm going to do. I saw this beautiful red Nighthawk 750 today and started thinking that's where I should be going. I wish Honda still made those today, I'd buy a new one on a heartbeat.