We'll things didn't go quite as good as I had hoped. After getting her all polished up she started leaking oil At first it was from the pucks and now I am not 100% sure where the oil came from so it's top end rebuild time. Pics to follow.
I'm trying to follow your thread.. First you had a no-start condition from electrical issues and it looked like the previous onwer had hacked up parts of your wiring. Sounds like you have that resolved. Then you said you cleaned a lot of things, and it sounds like you've been through the carbs because you talk about what the mains are and needle positions- but I didn't read if you'd cleaned the carbs thoroughly, got the floats right, etc. Also you mention timing isn't quite right, and the exhaust is non-stock (baffles removed), and now you're changing up the airbox..
No offense is meant with this- but, it sounds like you are changing an awful lot of things all at once- which makes it hard to measure what improves things and what tuning of carbs is right for the rest of the bike, etc. Also, you said there is oil leaking from the "pucks" (Caliper pistons?) and you're not sure, so it is top end rebuild time?! You already mentioned it leaked from the valve cover gasket- could that be your leak issue?
Maybe you've got a ton of experience with these bikes, and you're well within your comfort zone, but if not- you might be making change after change after change, frustrated at the bike for not running like a swiss watch, and then diving into motor work- which may end up being really expensive, and then upon re-assembly the best case scenario may be that the bike would run the same as it does now with all the unresolved changes you've just made..
If it were me, I'd just stop, and take a second to re-assess. Do you know if this bike ran before it was put away? If it did, then fixing the wiring problem, then cleaning the carbs and resolving any age-induced issue should get it back to running.. I haven't priced the air-intake boots in years, but that would be my next attack- fixing stuff that is obviously broken. Unless you're looking to make this a custom cycle without stock airbox?
Hope this doesn't offend in any way- I'd just hate to see you blow a bunch of money, or have this bike end up in 20 milk-crates when it sounds like you are close to having a runner now.
Jason