The 74 and up cars, which you obviously have are a lot easier. Rack clearances, motor mounts and radiator size options are not problems you will encounter.
There is the battery tray issue. My 73 was badly rusted so I just put in a new panel that was advantageous to a turbo. Options are the trunk or the drivers front (move the washer tank). Be aware of the alternator or other accessories on that side if you use the battery in the front.
There is a bolt (stud) issue on the outer exhaust where it turns 90 degrees downward. Shorten the stud as much as reasonable and possibly drill a hole to facilitate tightening. From there I used the stock T/C downpipe and had some clearance issues with the frame rail. Slightly flattening the out edge fixed that.
I have the 87-88 intercooler in my '73 and other than the scoop to feed the intercooler the hood closes without issue - BARELY and I do mean BARELY. Your engine has the taller center section of the valve cover and that might raise the air plumbing..
I used the fan motor from an MG (reverse the polarity) and have sufficient exhaust clearance. Some opt for the A/C model that puts the motor in the interior.
The T-5 has clearance issues (if you use the bell crank) with the cable and the crossmember. A small offsetting plate fixes that. The drive shaft is dependent upon the rearend used. I went from a /C-4/6.75" rear to a T-5/ 8" rear and the shaft swapped right over.
Mounting the fuel pump, return lines, harness etc. you just sort as you go.
I did a two part write-up on my '73 wagon swap using a stock '88 T/C engine - T-5. You might glean something from it.
http://www.fordpinto.com/index.php?topic=11908.msg76893#msg76893 http://www.fordpinto.com/index.php?topic=11909.msg76894#msg76894