pcm is the control module. If you look under the hood, all the wiring will centralize into a small metal box with several connectors that the wires are connected on.
I'd go for a newer 4.0L engine as it'll have less rust and lower mileage. There weren't any significant changes with the design of the engine block.
If you can, try to find a similar engine from a similar (newer) vehicle that's AWD and purchase the PCM. If you can get a deal on it, get the wiring harness too. This will limit any problems associated with check engine lights, etc. If cost is an issue you might be out of luck on finding an engine with lower mileage.
Check out Car-Part.com--Used Auto Parts Market
or RockAuto Auto Parts
If you want to spend a bit more cash, Jasper Engines is known for excellent rebuilds at a decent price for what you get with a warranty!