FWIW, I have found that these carbs need to be pretty much immaculately clean, or you get the exact problems you've described.
I don't know how many times I've pulled mine back off to reclean the pilot passages. This, despite running good grade gas, having inline filters, and a thoroughly cleaned tank which I also treated with phosphoric acid to 'reline' with a layer of Iron phosphate.
That said, since getting her dialed in, and buying gasoline only at stations which have 0% ethanol in the fuel, I haven't really had any problems. Not suggesting a chemical fix to what could be a mechanical problem, but it has reduced the headaches I've had in the past. I also made up new flexible gaskets on the engine side of the carb boots when I put it all back together, instead of the gummy red RTV mess that was the previous owners solution. Might not have made all the difference, but I don't have any air leaks, and it looks a lot nicer!
Good luck with whatever you get up on that 650. I know the litre boys will disagree, but having been on a few other bigger bikes now, I think the trade off between all out top speed, and the light weight and fantastic handling of the 650 makes it so much more fun.
Cheers,
Jon