Tried it again this morning after leaving it for 3 days, with the tank open to make sure it's not a vacuum problem in there. A cilinder firing here and there, a lot of backfires. It seemed to nearly start a few times, but only with the choke off. Does that tell anyone something?

I intend to clean the tank-filter, filter-pump, pump-engine hoses tomorrow, and possibly bypass the fuel filter. If that doesn't result in anything the next step would be to remove the spark plugs, check them, and try to deflood the engine. Any suggestions on other things to check while I have it disassembled again?

 

Well, I'm baffled. I decided to take the fuel system apart and clean it, but before I started I decided to try it one last time. To my surprise, it started almost immediately. Left it running for about 10 minutes, got my gear, and rode for about 15 minutes. Later that day I rode it for about another 30 minutes, and it ran beautifully.

Rather annoyingly I have no idea why. The only things I can think of is that I closed the fuel petcock some days before after trying, deep charged the battery, and stared with the tank open. But it seems unlikely that made the difference.