Yeah, I told Nate that he should try to eliminate one thing at a time.
I suggested he try to ease the idle screw in and increase the rpm's slightly from 1250 to about 1500 or so. Since twisting the throttle kills the engine, I wanted to see if increasing the RPM's via the idle screw would do the same thing. The reasoning: if the engine still stops, it's almost certainly a fuel flow issue.
Assuming that doesn't kill the engine, then I suggested he remove the in-line fuel filter and see if the engine stays running on throttle twist....ruling out whether or not the fuel filter could be the problem. Unlikely, I admit since the bike stays running while under choke.
If that doesn't solve it, then I suggested he remove the air box and try seeing what would happen with no air box on the bike, since he said the air box at one point had water in the bottom. This should eliminate the possibility of a clogged/water-logged air filter as a possible culprit.
You could be right that it's an electric issue but that also wouldn't make sense if it stays running under choke...the vibrations that would cause a switch to not work will be the same under choke or not.