So...if I understand you correctly, the bike seems to run fine during normal operation, but once left to idle, for more than a minute or so, it looses rpm, then stalls, and needs the choke to restart?
I would have said float height, but you have already checked/set the float height.
A couple of other things to check:
1. A slight vaccum leak around the carb manifold to head connections, and/or the manifold to carb connections. Usually this would cause surging at idle as well.
2. Air screw adjustment. I would richen them up somewhat. Not sure which way that is on the 400 carb screws.
3. Sync the carbs. Maybe they are not all set correctly. This shows up most at idle and small throttle openings. This along with air screws can make a noticable difference.
4. How's the compression? Low compression on one or more cylinders might be causing less vaccum.