I did a 5 spd swap in my '87 and found that it was actually fairly simple, just time consuming. However, there are a few things that can make the process go smoother, and I'd recommend them.
First off, I assume your BII already has an A4LD in it, which is the same length as an M5OD and 2" longer than a TK5. If you can help it, swap in an M5OD instead of the TK5 which means you can retain your stock d-shafts and don't have to move the x-member forward (however, the holes are already there in the frame). And yes, all Cologne V6s do have the same bellhousing pattern, but the 4.0Ls use a 3 bolt starter instead of the good ol' 2 bolt. I have heard you can swap these as the 3 bolt is supposed to be better, but I have never done the swap personally (check TRS). IIRC, the M5OD you're looking for should be behind most any BII or Ranger 4wd 2.9L from 88 or 89 - 92.
Secondly, most of the peddle ass'y is already under the dash, its just a matter of installing the standard peddles. You need to unbolt the steering column to do this, but its not overly difficult. The cross shaft they sit on is already there, and is compatible with the 3 peddle setup.
Thirdly, you need the floor pan that bolts onto the top of the trans tunnel, and it should come with the shift boot installed. Very simple to swap out.
Fourthly, you will also have to jump the neutral safety switch in the harness from the tranny. Its been too long so I can't remember which wires it is, but IIRC it was only 4 wires and was fairly simple to figure out. If you want to get fancy about it, you could even wire it up to the peddle ass'y to make it "stock" again. The other 2 wires should be for the lockup torque converter. I used the original auto computer even with the standard tranny, and never had any issues.
Finally, there is a plate on the firewall that you can screw your remote reservoir to, and the hole is already on the firewall for the master cylinder. Get the hydraulics with it and you're laughing. Oh, and it really wouldn't be a bad idea to take the opportunity to put a new clutch and slave cylinder in the tranny while its out.
Other than that, it should be fairly straight forward, it will just fall into place for you and it will surprise you how much parts are common. A lot of the issue I had was removing the rivets since I only had hand tools and a drill at the time, and was doing the swap with the truck stuffed in the corner of a very small shop. Without having to move the x-member, it would have been much simpler so for that I do suggest the M5OD since all you would require is just the tranny so you can keep your stock d-shafts and t-case. LR
