I don't get it. top in what way, if the motor is high how is that affecting the CG? is it a pod above the wing or you remounted it and the centerline of the crankshaft is now a half inch higher than originally. Did you re drill the engine mount or what. need more info.

if the crankshaft is 1/2 inch high it will more than likely cause two problems. The plane is going to want to pitch down becuase of a thrush-line issue not a CG issue and the engine will be harder to get going and keep going because now the outlet of the tank and the carb would be off.