First thing that comes to mind is Valve clearance. Next possibly valve timing (if you have rebuilt the engine without being a mechanic). Although there could be numerous other reasons for a backfire (e.g. blocked jets, carb synch, or exhaust leak.) Probably bet to try and get a mechanic to look at it as it will be next to impossible trying to give advice without actually being with the bike and hearing at what stage she pops or being able to do a few checks.
