What kind of problems do you think I would have swapping in a 97' A4 into a 94'? I'm guessing that the OBDII on the 97' would affect it in some way.

 

The plugs are in different areas making it hard to put in. Your best bet is to get a 94, and put it in the 94. 1994 was the weird year where transmissions from other years don't like to be swapped into them, unless it's a manual. I think the lines attach in different places too.

 

I knew there would be something odd with it. Seeing how it was the first year of the 4L60E. G.m. is always changing something.