CAD:

With the Great Planes mount, the center of the crank should be at the center of the mount no matter which way you turn it. You seem to have done everything right.

I guess all you can do is measure how far it is off, then knock the blind nuts out, fill the holes with short pieces of dowel and redrill that much lower. I've had to do that on my last two Great Planes ARFs even with the engines mounted sideways. Don't know why.

Jim