It will physically fit. Make sure if you have a 2WD truck, get a 2WD transmission, 4WD truck needs a 4WD transmission.
Are we talking about automatic or manual?
Later model A4LDs had changes to the valve body including going from one solenoid to two. If you are going from a single solenoid trans to a two solenoid trans, you may need to swap the valve bodies or figure something out on that. Not sure if 91 had a single solenoid or not, but there are differences in the valve bodies from year to year.