Sounds like you're running lean on the pilot.
I've got a 93 Supertrial, basically the same bike. 240 motor. Same lights, horn, and brackets for passenger pegs.
Double-check the carburetor. Mine has a Dellorto PHBH, not a PHBL, and it'll clog the pilot jet if I even look at it funny. Difference is air screw versus mixture screw. Drop the bowl on the carb, pull the slow jet, and run a fine piece of copper wire through it. When the pilot gets partially clogged, mine has exactly the same symptoms as yours.
Whereabouts in upstate NY are you? I'm just outside of Troy, and hoping that the snow will melt in the yard in the next few days. Got some riding in last weekend, but we've been socked in with snow since Tuesday.