Stumbles off idle, then surges
 

The story thus far: bought 2 months ago, it ran fine for about 15 minutes until it started overheating. Turned it off, trucked it the rest of the way home. It sat while I worked on the plastics, got water in the fuel. Cleaned the carbs with cleaning and a guitar string.

Got it running 2 days ago, rode up and down the street. It stumbles coming off idle, then picks up and maintains RPM for a several seconds after I close the throttle. Let it run for about 6 minutes and it still wanted some choke on.

Thoughts?

Are you sure you did a thorough job of cleaning the carbs? To me it sounds like you might have 2 separate issues. The stumbling off idle and then continuing to need choke suggests to me one or more of your pilot jets are not completely clean. The keeping up the revs after you've released the throttle coupled with suddenly surging off idle makes me think one or more of the sliders /needles are sticking. That's why I started by asking whether you're sure the carbs are really are clean. I've recently been through mine and it took several attempts to get them truly clean. Also, could you be getting some contamination from the fuel tank? Is it clean inside (no rust), and do you have a fuel filter fitted to catch any nasties before they reach the carbs?

I have a similar problem (It doesn't really stumble from idle but takes a few seconds to get back to idle), only it's much more intermittent. Found that my isolator boots for the two inside carbs were flattened on the bottom. Also, I didn't completely disassembly and clean my carbs, just did the common symptomatic areas. And it's possible that a vacuum problem may affect the opening of the slide/main jet needles. We'll see when I get it back together...

I agree that it may be more than one problem. The stumble could be poor fuel (ethanol separation from sitting) or maybe slightly plugged pilot jets. Head pipe leaking causes stumble also.
The more probable cause is a vacuum leak. A vacuum leak would create a lean condition and maybe that's why you need to engage the enrichners. If the carb sync is off, an open butterfly would act like a vacuum leak. One symptom of a vacuum leak is the the high rpms when the throttle is shut down and it takes time before the engine rpm drops.

So is there vacuum beyond just the intake runners that I need to worry about?

Carbs were definitely still clogged. Rode to work today with an inline filter installed and a fresh tank of gas + Seafoam, got progressively better and now is running like a champ up to 7k where it starts to stumble. Progress!

Sounds like you've made some real progress from needing to keep the choke on, and the low rev stumbling - seems like the pilots are OK. I'm not sure whether you've dynamically sync'd the carbs or not? If not, I'd make that the next step, as well as checking for vacuum leaks around the boots.

Haven't sync'd yet, will probably approach that soon. Bike now runs well enough to get frighteningly hot when stuck in traffic. E-fan sounds like the bearing is going, will need a replacement (upgrade?)

Okay, after several tanks of gas this still persists, and also the engine breaks up completely at 5k.

Have you had a carb sync yet, a proper one with vacuum gauges? If that does not help a full carb clean may need doing.

If it needs choke, its to lean. The low speed jets may be clogged. How about the float levels? Have you checked them?