1997 Yamaha Virago 1100 cc

Recently, after having found a seal that needed replacement in the motor I decided to redo my engine since the heads were off and as I was going to keep the bike for a couple more years and thought I would have no problems however, this is not the case before the 1000 km break in period the problems began, first it was when I came to a stop in traffic or at a light the motor stopped, they adjusted the fuel and this seems to have worked, Recently there seems to be another problem when after riding (61 KM) the bike now seems to want to stop and backfires while running then it restarts, the carbs were cleaned, gas filter was changed, plugs were changed and a bypass of the Kick stand was done. I was wandering if this has happened to others bickers and what was done or what did they replaced to fix this problem. Ron