The bike ran great on the freeway all the way to the exit. It stalled at the exit light and then again when I pulled into the parking lot a couple minutes later. We've had a couple of 85-90 degree afternoons the last couple of days and the bike runs really well when it's super hot out.
This mechanic that I'd spoken to on the phone discussed what I'd been going through and then he took it on a test ride. Said that he'd seen another bike similar to this and it ended up being the ECU, although he kind of grimaced at that ($$$$) and he said that the problem sounded unusual.
He took it in the back and ran an Exhaust Gas Analyzer test. Hydrocarbons looked pretty good with one side a little high, probably due to the jerry-rigged carburetor cap repair that we made (have the panew part, haven't gotten it on yet). The idle mix screws were still capped. He was quite impressed with how well the carbs seemed to be dialed in when it was running (thanks to my friend's handywork).
Bottom line, it isn't carburetion. He thinks it's either the coil pickup (simple repair) or the ECU (about $1000)

Being an engine engineer, I'm plenty familiar with EPA warranties so I looked it up in the owner's manual. Basically, the emissions warranty is 5 years/18,632 miles. Looked up my records. The bike was purchased 5-13-00

So I'll be arranging to take it in for the full exercise. If it's just a pickup, they'll do a cheap repair. If it's the ECU, it's under warranty. Thank heaven I didn't wait until Monday!
Sorry that EPA warranties don't help you parsley1938, but at least you know some kind of direction.
Onward and upward.