Only thing I can think of is there could be a difference in the taper on the shaft of the steering box for certain years. Made it sligltly larger. Would have to look at the parts book to see if that shaft part number changed at all through out the years.
Your only talking 3/8". Center link is held by both the arms, it will bolt together no matter what the height of the arm is. Height difference is either going to pull the wheel in or out slightly on that side. It would be corrected by the tierod adjustment at alignment.
Pretty sure my centerlink is dead nuts level, I can check next week when I go back out to the shop. Stick a bubble on yours see where its at.
The alignment shops deals w/ this **** every day. I'm sure they will know right away whats up. I wouldn't sweat it.
Freight company called today and said my custom steering setup is scheduled for delivery friday
Fingers crossed those guys built the **** exactly as I specified