750 sxi performance issue

I have a 750 sxi w/ 795 big bore, kommander industries head w/29cc domes, factory dry pipe, msd enhancer, and dual riva 48 buckshots. As soon as i purchased this ski it ran away on me so i overhauled the engine w/new crank, seals, gaskets, rings, and head o ring kit. Trying to get it running and it will start right up but sometimes it'll backfire through the intake and it wont run or rev properly. I suspect an issue with the msd.
 
Not likely that i sheared the key but its always a possibility. I'll check that then I'll switch out the ebox with my other stock unit and see if the problem follows the msd box
 
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