Now I have seen the set up, the only real way is to clock the unit square to the axis.
Why!
I will tell you, grooves will have tapered sides, threads will be at the wrong angle and parting off and drilling/reaming will be a tool smashing extravaganza.
You can program out tapers in faces and in diameters but coordinate rotation can not fix this. Lathes must move parallel and square to the spindle or you are in big trouble.
My solution would be :-
A little bit of accurate setting the first time and then fitting taper dowels. This will allow you to refit the unit at any time with the same accuracy.