You need to do a bit of sleuthing to work out what is wrong.
I would mount the axle with the shaft sticking straight up in in the air and watch the shaft while rotating it. It should spin straight and true. If it is not straight and true, it needs to be straightened until it does run straight and true.
I would then lower the torque tube over the known straight shaft and look at how it aligns to the axle. I would rotate the TT and if it is out of alignment, the end will always be out but rotating with the torque tube. (Hard to explain). If it does not align, it needs reworking until it does.
If it does align to the axle radially, then you need to see that it closes to the axle squarely, contacting all the way around at the same time. If it does not, that means the flange is not square and that would need attention.
If you have to push or pull anything to get it to align, it's not right.
Mart.