Set aside a day to shim the subspindle and get those tool positions tuned in to .0002" or less.
If your bores are off, your sub to GB is probably off too. Get the sub to GB dialed in first, check the bores on each side, get those to zero up and down and then comp the side to side in the X axis on the control. It's not a big deal to losen the sub and shim it, loosen only two bolts at a time. Measure meticulously and when you have it, take everything out, put it back and measure again. There is a keep relay to flip (at least on a fanuc) that puts the machine into alignment mode, which makes alignment much easier.
These machines can be so accurate, it is a shame to run them with mis-alignments, IMO.