Thanks, everyone. I was wondering about the new petcock. My old one was definitely going, the bike was hesitating on acceleration, idling crappy etc. (I did have the carb re-jetted and the airbox removed etc. already. I didn't have to choke it to get started after that. It does run better with the new Raptor.
I did start shutting it off after I ride it, I'm wondering if maybe I should shut it off a few seconds before I shut the bike down and see if that makes a difference for possible flooding. I did stuff all the openings, so I don't think it is water in the case. I may change the gas since I did drain it into our lawnmower gas can to change the petcock. It looked clean, but you never know. I'll definitely do a valve adjustment and check the pre-adjustment gaps. If that doesn't work then the sealer in the oil.
Mileage? That's a mystery, it's a used 86 engine in a 2005 frame, the previous owner claimed "low miles". That's why I checked the tensioner. It was about 15mm out. The shop I took it to to replace the oil seal in the head said the cam and jug looked good, so no blatant signs of high mileage or abuse. I put 20-50 Mobil synthetic oil in it so it shouldn't be too thin for our weather.
And yeah, noises on an aircooled engine can drive you nuts. My old VW's were always talking to me in foreign languages.