Howyadoin,
I decided to check the pilot screws. I found the following:
Carb #1 - 5 full turns from seated
Carb #2 - 4 full turns from seated
Carb #3 - 6 full turns from seated
Carb #4 - 7 full turns from seated
I seated them all and set them all to 2.5 turns out, it seems to be running quite a bit richer, I'm getting a lot of gasoline smell in the exhaust. Does that make sense, does the mixture get richer the closer the screw is to the bottom? It's still not running smooth. #3 seems to be particularly bad, I think I'm getting some backfire up through the carb. I sprayed WD-40 around both sets of boots on each carb, both in front of and behind the carbs, and saw no change in idle.
My next steps are to check the mechanical advance and check valve clearance. If those are both OK, then it's time to pull the carbs and clean them, and replace all the carb boots while I've got them out. If the valve clearance is out of spec, I'll have to order up the lifter holder tool and some shims from Z1.
Another problem is that I don't know precisely what mods have been done to the engine other than the increased displacement (1000 to 1100cc); are the cams original, et cetera... The thing that really bugs me about that is if I decide to send the carbs off to someone like wiredgeorge and he rebuilds them and sets them up, I have no guarantee that I won't have to do more fiddling when I install them because of some unknown mod.
I'm beginning to see this as an off-season project
I was hoping to get the bike stable for the remaining 6 weeks of riding season, then dig into the carbs, valve stuff and whatnot over the winter, but I can't even get her running well enough to feel comfortable or safe at this point... I'm not giving up yet though, dammit...
Thanks everybody for your help so far, I'm going to keep trying to get this right, both for myself and for anyone who finds this thread sometime down the road and learns from it. I'll let you all know what I find on the valve clearance and mechanical advance items.