Blown engine replacement

Hi guys i was involved in a hit and run . Wrecked my 2011 vz800 l1 engine, a bike mechanic said he would rebuild the engine. Bottom end shot to bits. 
Said it wasn't worth fixing.. 
So he bought a replacement engine, now it turns out my engine had 4 spark plug this replacement runs 2. He said he hadn't noticed when he bought it, obviously an early model engine. 
He has fitted it but now running sort of , its not firing the back pot properly, im not a mech myself but trying to get it sorted, so he can get it right, or maybe i will have to do it myself. 
1 Does the 2011 loom run wasted spark or 
controlled
2 is the loom and ecu capable of running the engine

3 is there a way to retreieve the fault codes

Thank you gang