Usually people want to swap in a manual trans and get rid of the automatic, but to each his own.
You can not convert a 2WD A4LD to work in a 4x4, so you will lose transfer case and 4 wheel drive
4WD A4LD used a shorter Main Shaft and tail shaft, so while you could rebuild the whole trans and buy and install the shorter shaft and get the 4WD tail shaft.
It would be way easier to find a 4WD A4LD and rebuild that.
You need the computer from the '89 to run/shift the A4LD, 2WD or 4WD didn't matter
Transmission mount is different, so you need one for A4LD
And new Drive line for 2WD unless '87 is extended cab as well
Floor shifter would probably be best, since there is a hole there now, have to be a Universal cable shift model, stock would be hard to find, or you could change out steering column to get column shift automatic
Need to change pedal assemble, not required but for looks