As an update, I made the following changes which by and large resolved the issues.
It seems that the high idle was due to a vacuum leak which was fixed with new carb boots. Check that off the list.
I corrected the problems with the butterflies by re-aligning the carbs. Problem fixed.
I had it running, but soon after it would not start. I found some very small debris when draining the tank which clogged slow speed jet, pilot screw opening, and accelerator pump check valve. Aside from rinsing the tank several times with gas, I did a thorough carb cleaning with chem-tool carb cleaner spray, e-string, and compressed air. It seamed to do the trick. I set the idle mixture screws at 1.5 turns out which I'm not sure is the right starting point for KEIHIN VB44c carbs. The mixture screws are on the air side.
Here's where I'm at today...
Starts cold with full choke, runs with no choke after 30 seconds or so. Idles at 900rpm, although somewhat labored, occasionally stalls with no throttle. There's a stutter or lag with initial throttle, but then it picks right up. All cylinders seem to be equally hot when checking the exhaust pipes.
I'll put a couple of miles riding in then check the plugs, right now its been ridden less than a mile. It seems to be running a bit rich, other than adjusting the mixture screws and a proper sync, I'm at a loss.