Thanks all the advice and info it was useful and I know much more about how carbs work now. Stock pilots back on and so far so good. Everything was still clean in there, I just touched up the stock pilots that were in the used parts box, checked the passages and float level and put them back together. Was a beast to get started - probably because the brand new plugs were now toast, but once started and warmed had no problem rolling from no throttle all the way up. Still sticks on advance a little longer than it should, but unless I had just gone through this I probably wouldn't even notice. I'll do a little bit of tweaking the mixture, replace the plugs, and expect this to be behind me. Just in time for bfire next week!
Without ebay it'd be near impossible to get this bike running, but some of the stuff I got there has caused the most trouble (clutch cable, carb kits). Seems like a post about thoughts on what you can get from ebay and what needs to be genuine parts would be helpful to someone like me.
For future reference if someone has a similar problem and stumbles on this:
Current (working) set-up - 100 main jets, 40 pilot jets, needles in third position, air screws 1 turn, 4-1 exhaust, stock airbox, dyno ignition and coils. First, pull off the bowls and see if you have the aftermarket pilot jets that are smaller with very small holes. If so, replace them with the stock version, put your bowls back on and you might not have to wrestle the air box.