Basically if the valves opening/closing are out of time from what is intended, you would run the risk of hitting a valve with the piston top at worst case, or compression in general being lower than normal, at best case of incorrect valve timing.
I haven't looked at the wiring diagrams in depth, but double check that the low voltage leads to the coils are on the correct coil. I suspect they are probably correct as it runs somewhat, albeit not good, but it does run.