Well I've considered writing a bit of a manual about this, but simply havn't bothered yet.
Maby this will induce me to get on with it and write things up. For now here are answers to your questions:
First define what your objective is (My objectives

1)Get my vehicle back on the road at a "reasonable" cost.
2) Maintain Manual Transmission. This is my preference for wheeling and fun driving (I don't like the Auto trans., but they have some nice advantages).
3) Build a reliable engine, starting with a explorer 5.0 or a 91 - 93 TBird / Mustang engine. (I figured an Explorer engine would have the best accessory bracket set up and lower miles so it should be in good shape - no rebuild required)
4) Low end torque were my objectives as I use the vehicle off-road, Not top end HP.
For the questions:
Transmission:
The M5R2 Trans. comes in at least two flavors. One for The older Ford engines like the 5.0, One for the new modular Ford engines like the 4.6L. They have different bell housing bolt patterns and are not interchangeable.
My solution was to use a rebuilt M5R2 for the 5.0 engine. The Transmission shop helped me with the cover plate issue. I was poking around in their shop and said I wanted that transmission, but this other cover plate if possible. I must have run into the right person who took it on as personal challange. Just about everything inside the two versions of the R2 are the same EXCEPT the shift cover plate, and the shift forks. When the Modular engine first appeared the shift forks were identical to the ones found in the older R2 for the 5.0 engine. After about a year or two of production they switched to different shift forks made of aluminum, and they wrapped further around the gear.
With a little hunting through their scrap pile they found the right cover plate and we tried to swap it.... Everything worked out. So now I had an old version R2 trans. with a newer modular engine cover plate. NO internal components were swapped out
2) Forget transplanting the entire F150 drive train. The transfer case is quite a bit larger and will require re-indexing to drop it down, and/or frame modifications. As mentioned earlier in the post Advance Adapters makes an adapter to mount the the BW1354 T/C we have up to a full size ford transmission. All the full size trans. have the same 6 bolt pattern and indexing.
3) The T Bird engine is a good swap candidate. Not because it is lower, but because the accessory brackets / water pump are shorter. Overall engine length can be a problem. There is limited room in the X. In my opinion the Explorer 5.0 is the best candidate because it has the shortest accessory bracket set up, the "truck"Cobra intake manifold, Truck - higher torque cam, and 65mm TB. (If I were to use a mustang or TBird engine I would have wanted to buy these components to meet my objectives of a low torque perfromance engine.
4) Using the Exoplorer engine does require a few simple modifications, assuming you intend to use 91 - 93 EEC IV system.
a) The intake air temp. sender port must be tapped into the lower intake on the #5intake port. There is a "flat" on the manifold for this purpose. It is simply a matter of drilling and tapping a 3/8" pipe fitting here.
b) The electronic iginition on the explorer must be converted to a Distributor ignition system. This means acquiring the right distributor (91-93 Mustang or Tbird roller cam distributor - $50) and a compatable coil ($5 used, $45 new).
Note: The Truck intake manifold does produce better torque, BUT it will not fit into the X without major hood modifications, such as a 4" scoop to add the necessary clearance.
5) I did not want to deal with the hassle and potential problemns of using a "used" wire harness. I purchased the Ford Motorsport Hot Rod Harness kit - Main harness, engine harness, O2 harness, and sensor package.
I will send along my sporeadsheet shortly.
Guy