If I remember correctly, you have to worry about the clutch lockout (on an automatic, it has a jumper, if you want it clutch lockout you will need the switch)..
I "think" also, there was a plug to put in the connector that normally goes into the auto tranny, but I can't remember exactly what I read, but I'm almost positive I read it on this site.
Also, if you don't change your computer, you will need to either keep the solenoids from the a4ld (there are 2) connected to the wire harness, or just use two 23 ohm resisters on the wire so the computer still thinks those solenoids are working (I've done that on my X with the 700r4 swap).
~Mark