So, an update!
This thing is still definitely haunted.
When I can get it to run right, it runs like a champ. The problem is that it's hard to keep running when the mixture screws keep backing out of the carb bodies and falling off. I haven't lost one yet, but the last time I took it out it started running like shit and when I finally got it home I discovered that the mixture screw on carb #1 had backed all the way out again and was balanced precariously there on the carb body. These are K&L aftermarket mixture screws, so I changed out the o-rings with ones that are a little more robust to A: seal them better and B: make sure they don't back out anymore. Fingers crossed.
I also failed to bleed the rear brake properly when I first reassembled it, so I have to do it again. I hate this rear brake system. The one on my XS850 (which is damn near the same) is easier to bleed. My Mitivac hand pump was broken, so I was trying to bleed it the old fashioned way (with the caliper removed, dangled over the swingarm, and clamped to an old rotor I keep around for this kind of thing) and it absolutely refuses to bleed. I have a new Mitivac on the way.
Also, something weird is going on with the speedo drive. I swear that I can see it moving inside when I turn it by hand, but it doesn't turn the speedo cable. I cleaned it up and greased it, but it seems like it's not engaging the drive washer. At this point I may just pick up a new one, they're cheap enough on eBay.
So, yeah. That's where this build stands - the constant fiddling zone.