FWIW I checked the valve clearances this morning. They are not the problem. I was really hoping that would be the problem, since it's something I can easily fix.

The exhaust are both between 0.0714 and 0.08mm (my closest feeler gauges).

The intake require a little guessing, since I could not fit my smallest feeler gauge in there. They are under 0.04mm but the shims spin freely in the buckets which should indicate at least 0.02mm but regardless, the fact that the exhaust were spot on and the intake are close makes me think this job has been done relatively recently on this bike. I wouldn't mind having more clearance on the intake side but this shouldn't be causing the problems I'm having.

Soo... with that, once I put the bike back together, I am taking it to a shop. As soon as I can get confirmation that they can look at it promptly, I'm going to ride it over and leave it. Maybe someone has seen this problem before.

A few hours after I left the bike at the shop, I dropped by to drop off a spare part and the owner of the shop said, "hey, I think he's found the problem with your bike, and he's working on it now."

The shop owner took me out to where the mechanic was working on it. He had it apart, carbs on the bench. He said the problem was that the float needles were not sealing all the way when closed, so once the bike was warmed up enough to not require choke (which, again, takes 10-15 minutes of riding on the road!) then the engine could not use fuel as fast as it was being delivered through the leaking float valves so it was flooding at low rpms. At high rpms it was burning fuel fast enough that the leaking float valves didn't matter. He had put in new float needles. I decided to hang around the shop a little while since they were likely to get the bike finished and I could just pay them and then come pick it up later in the evening.

While I was in the shop office talking with the owner, the mechanic came into the office and told me that I didn't need to hang around, he was going to have to keep the bike until tomorrow. He said while he was setting the idle speed and mixture the bike just died, and wouldn't start back up. He checked the carbs and one float bowl was empty. So it's back to the drawing board. He's hoping it's just junk from the tank clogging something in that carb. Could be, I guess. I've had this happen before and it was a sticking-closed float needle. Either way I'm confident they will fix it and I'll be back on the road by the weekend.

Welp, the shop just called and he says they got everything totally sorted and while he was trying to dial in the idle mixture and idle it just wouldn't run right. That's been my experience. So he checked the compression and it's low on both cylinders, one is extremely low. I told them to go ahead and dig in and figure out what the damage is, and they found that the intake valves were leaking badly so it is going to at least need that fixed. I elected to have them hone the cylinders and put rings on it while it's apart in addition to cleaning up the valves and head, and the mech also wanted to do a little mild porting while the head is off to smooth some rough spots, which he says will improve throttle response and make it easier to dial in. So I'm now waiting for them to finish a top-end rebuild.

I suppose that's not terribly surprising on a 25 year old air-cooled motorcycle with 21K miles on it.

Even though this is going to be a lot more expensive than I was hoping for, it is somewhat vindicating to know that I was not completely incompetent. They assure me that this will absolutely fix it and it'll be good to go for a long, long time. I'll also be glad to get this fixed right once and for all.