In terms of physical dimensions, an '88 A4LD and a '94 A4LD should be identical, and the 2.9 and 4.0 use the same bellhousing bolt pattern. '88 was the first year for the 2 solenoid valve body, so the electronics should all bolt up just right. Though, with transition years like that, you'd want to verify that the '88 has two solenoids in the valve body.
Stock, the 4.0 A4LD was built a little stronger than the other engines. However, many times when an A4LD is rebuilt, they'll rebuild it to the 4.0 specs anyway with the upgraded parts. Only your rebuilder can tell you if they installed the updated parts for a 4.0 or not, though. If it was rebuilt to 4.0 specs, I'd say put it in. If it wasn't it will still fit in there, it's just a question of how long will it last (but isn't that always a question with an A4LD?).
