The 5-speed swap is fairly straight forward.
As far as electrical/electronics, you need to take the Park/nuetral wires on the auto harness and solder them together to close the circuit, and the wires for the reverse sensor need to be taken and connected to the reverse sensor.
The computer should be changed but it is not 100% necessary. Auto computer and manual trans will have a check engine light because the converter lockup circuit is missing, and it may run a bit funny since the idle strategy is a little different, but it will run and should be perfectly drivable. A manual trans computer also will generally have a bit more aggressive tune to it.
The A4LD, FM145, and M5OD are all the same length, so the trans crossmember will already be in the correct position. Even when dealing with an FM145 the holes are already there, you just have to pop 6 rivets and move the ears.