Welcome to the site !!
I am a bit concerned that the valve hit the piston and they found no damage to the crank bearing , if it hit hard enough to bend , chances are it made a flat spot in the connecting rod big end bearing....maybe you got lucky , but i would be concerned and hope they will stand behind it it if goes , since its basically their fault the valve hit the piston , i would think they would have just replaced everything..... hopefully you did not sign anything saying if something else happens they are not responsible , i personally would have made them replace EVERYTHING including all bearings , crank/rod assembly , piston/rings all with new matching components of what was there when it blew apart ...hope i am wrong ....but i have seen a valve hit a piston before , show minimal damage only to have the rod bearing fail shortly after .....just be prepared and get something in writing before continuing much further , otherwise it "could" be a major expense out of your pocket because of their doing
With that said:
The backfiring issue can only be a couple things , it is either the timing IS off and your not catching it , or its a fuel issue or a massive air leak (gasket sealing or valves not seating as described and leaking past allowing a lean condition) , since the bike presumably ran fine before the rebuild and directly afterwards until the valve cut loose , i will stick with a timing issue first
Cam lobes facing 2 o'clock rearwards , 2 slash marks on cam sprocket level with head like so - - , large round plug on clutch side has arrow and dot lined up facing each other , and ignition cover small round plug with mark , also make sure there is NO SLACK in the timing chain , if there is , all 3 marks will not line up and your timing will be off as the engine rotates ... also make sure tensioner is functioning correctly
Start with double/triple checking the timing is in fact 100% perfect , something has happened between first tear down and re-assembly this time , if you are the one doing the work then just take each step and confirm each item is as should be , it has to be something you did or did not do and are just missing/overlooking it , it happens a lot , just confirm each step is correct and move to next one ,,,,,,,,,,report back with results...