So now I have my bike working in a somewhat decent order, except that I am still have troubles with it running well.
I think what WiredGeorge had thought earlier might have some play in this problem, but I will ask to make sure.
When I start the bike cold, it runs mint. Starts right up, sounds nice, revs nice, real zippy too. About 2 minutes later, I'm pretty sure cylinder #2 stops firing, and the bike starts running hard. Almost like it is bogging, full throttle almost kills it, sputtering like it is choked, also I can hear what resembles air whooshing somewhere. Weirdly enough, when I let it rev down for a few seconds, and then re -rev it, it is good for a second or two, then sounds like a lawn mower engine again, almost dying.
Reason for suspecting cylinder#2 is that after running it for a while, I noticed it is not as hot as the other pipes, and the spark plug in it, looks 3 times newer than the other 3, all were replaced at the same time.
For anyone that didn't follow the other thread I had the last week or so, I have checked the compression and all cylinders are very similar, showing minimal ring wear. So compression is relatively good. I am wondering if this is related to the valve or whatever not closing enough when it gets warm or something. It seems to be related to when it has warmed up a bit, though maybe that is just random..??. I have also check for a spark on #2, it has spark.... I don't know how "good" of one, but it definitly has spark and I know that the firing order is correct.
Thoughts??
Thanks again to all who helped before. Great job.