I've done the swap a few times, using stock mechanical linkage. I assume you are talking about a 4 speed toploader (vs the 3 speed.)
The crossmembers are the same. No modifications are needed to the hump or the shifter opening, as long as you stay with either a stock Ford shifter (yuck) or get a
Hurst Competition Plus (recommended.) Nothing on the body should need tweaked.
The Toploader is tough as nails and will need no strength modification to live behind a hot 289/302. Except for the input shaft and output shaft, the same guts and casing are found behind a 428CJ and the Boss 429.
You will want to purchase a Toploader that was made to fit a Mustang. Including the bellhousing, it will be the same overall length as your C4 and will have the correct mounting location for the shifter on the tailshaft. As long as the toploader isn't one of the early 64/65 type with a 25 spline outputshaft, your C4 driveshaft will work just fine. If you go here:
http://www.davidkeetoploaders.com/idchart1.htm you will be able to match the toploader ID to its original application. Poke around on that site and you will become quite knowledgeable about the toploader.
Toploaders come in 2 basic flavors. A wide ratio and a close ratio. I recommend holding out for a wide ratio as it's lower first gear is desireable.
Although it may be considered overkill for you combination, I am very pleased with the Centerforce dual friction clutch. Low pedal effort, smooth engagement, and can handle brute force when needed.
One thing you may not have thought of is the speedo cable. Although the cables are generally the same, the one for the toploader will be longer as the speedo cable normally enters on the passenger side vs. the driver's side for a C4.