Automatic to Manual wiring instructions for a 2002 Jetta Wagon TDI: (should work for all A4s but YMMV)
Pop the lower dash panels off and pull out the relay panel.
Find relay 175
Cut the red/grey wire and red/yellow wires and ground them.
Now you get to decide how you want your car to work, and wire accordingly.
Cranking options:
1) To start only in reverse, but still with no clutch safety switch just follow the engine bay instructions below
2) To start with no clutch safety switch, but also no gear requirement just connect the yellow/blue to the green/black on the back of relay 175.
3) To crank like a normal manual (no gear requirement, clutch must be pushed in) then connect the yellow/blue to one side of the white clutch switch and connect the green/black to the other side of the white clutch switch. * NOTE: Do NOT cut the green/black or yellow/blue but connect into them.
** Note: I'll leave the method of connection up to you. Some prefer to remove pins and insert new wires with pins properly into the harness, some prefer to solder, some may want to try clamp-on connectors. I went with the soldering method personally, and won't get into a which is best debate which I'm sure will ensue.
Now Go to the engine bay
Pull the airbox access panel by removing the 4 phillips screws and sliding it out and up.
Slide the TCU connector off by pushing the handle on the driver's side of the TCU toward the driver's side of the car (it is a sliding lock)
You can remove the TCU and try to ebay it, or just leave it sitting there.
Located in the wiring under the airbox area: take the transmission switch connector (pictured many pages back), and using your method of choice connect the yellow/blue wire to one side of the manual transmission reverse lamp switch. Connect the green/black wire to the other side of the transmission reverse lamp switch. (reverse lamp switch also pictured many pages back).
Tada! That should be it for the wiring.
I need to go back out and test my new clutch safety switch idea, but I see no reason at all why it wouldn't work.