I may be wrong here, but I think the sequence of machining is wrong. The backs of the wheels should be faced off, each in turn to gain a reference point, then rotated in the chuck and tapped against the jaws to seat it, the rim of the wheel can then be clocked in, so it runs concentric, then face the front of the wheel centre, and drill and ream the wheels bore. This means that the rear and the front centre and bore can all be trued up to one another, the wheels can then be mounted onto a mandrill and the rest of each wheels tread machined. Along with crank webs balance weights.
You say that you've been using a MT3 arbour turned to fit the wheels bore. This should mean that the wheels are constant with their alignment. All I would say is to add support to the mandrill by using tailstock support. That way when machining the rear of the wheels tread the mandrill is not likely to move out of the spindle.
I hope this is of some help
Sorry just read the post above
Edited By Jon Cameron on 29/10/2017 11:31:42