Ah, I think if i remember correctly there was a difference in wheel orientation between the older wheels and the 90-93 wheel setup. The momo adapter is setup for the 84-89 steering column, but when used on the 90-04 column, does result in the steering wheel being offset a few degrees.
The BEST way to fix this is the MM steering shaft, which allows you to clock the wheel without moving the rack. (step 25 in the procedure) If you center the wheel and then adjust tie, you end up with the situation you describe as the rack isn't centered to the wheel.
If your solid shaft is the MM one, follow step 18 to 31 exactly, and then take the car to be aligned. I can see why the shop didn't center it as it involved taking the aftermatker shaft apart to reclock it.
If it's a different brand shaft, it may not allow you to reclock the wheel