Update
I rebuilt the top end due to a crack in the bottom cylinder which I replaced. I have the bike running now, I cant seem to get the bike run and idle properly though. I have rebuilt the carb and cleaned it a few times now and even bought carb rebuild kit. I got it to a point this past weekend where it would run with out the choke out which took a bit of tweaking with the carb. I have ridden it down the street and it sounds like its choking and not getting enough fuel. There is fuel in the line, I have adjusted the throttle pin to run more rich. I order a few different size main jets to test, but I am running out of knowledge, skill and ideas.
Any input would be appreciated. Thanks