Dan,
No need to post photo's since if all was fine before on the mechanical side then it should still be to you standard.
Since you post two problems, how about eliminating one by taking the shuttlepro out of the problem and then simply
swaping the x,y or A axis for the Z axis, since they are working correctly, and see if you can narrow things down.
Don't have a g540, but assume your wired thru correctly, have followed Gecko info on motor info and, and that the
current set resistor is giving you the equivilant torque that you had before.
RICH