Take out both shafts and roll them on a piece of glass. You will be able to compare them and see any difference in how true they are.
To check the couplings just swap them over and see if the problem moves from one shaft to the other.
If the problem persists you might suspect the motor (very unlikely) or the tube.
I have seen a coupling where the hole was drilled and taped off-centre. If you have one of these just replace it.
Chas