'85 to '87 A4LD's have 1 solenoid (TCC) in the valve body. '88-'94 A4LD's have 2 solenoids (TCC and 3-4).
2.8/2.9/4.0 share the same bellhousing bolt pattern. Other engines are different. As I understand it, the A4LD has a removeable bellhousing, so this may not be a major consideration.
4x4 and 4x2 transmissions have different output shafts and tailhousings. You can convert from 4x2 to 4x4, but it requires a complete teardown and replace the tailshaft (which, I'm guessing, is what you are trying to avoid).
Finally, over the years, as weaknesses became apparent (and as the 4.0 was introduced), internal upgrades were implemented.
For the easiest, most reliable used replacement, get an A4LD (4x4) from a 4.0. If you find one from an '88+ 2.9 that you know has been rebuilt with the 4.0 upgrades would also work (but it would seem pretty rare to have that much history on a used transmission). Any '88+ A4LD from a 2.9 will work, but it will be a weaker replecement unless it is rebuilt and upgraded.
That's about it for "plug and play" replacements .As far as other transmissions:
C3 was the precursor to the A4LD, and can be used -- recognizing that it is a 3 speed transmission without overdrive.
With expensive or custom built adapters, other transmissions can be used. Most common is the GM 700R4.
The M5OD is the most recommended manual transmission swap.