Hi Rob,
Dropping that motor out & having a good look into it on a bench would more than likely save you alot of grief....believe me, I know this 1st hand.....with my XT6.
Nayruf is on the right track by suggesting you check into the valve timing first.....if your tensioner was missing when you got it.....good chance that cam-chain has jumped a tooth. Not a difficult task to correct....plus, if the motor is out of the frame, you can check the combustion chamber easier.....and have a look into the clutch while you're @ it. Pull those clutch plates apart....clean & re-oil them before re-installing.
Regarding the carb.....make sure your choke is working properly as well.....tends to help more when starting cold.
Also, make sure & get a tight seal @ the intake rubber.....can also cause back-firing.
Don't get discouraged.....it's well worth it in the end.
Good Luck