I'm late at posting to this thread, but I have researched this situation for a 66 Mustang C4 to T5 swap. I would try to find someone else that has successfully done this. I know that on my car there were header clearance issues with the cable clutch and that there are issues with the mechanical clutch. These can be worked around. If you plan on installing a power brake booster there can be clearance issues too for the cables or mechanisms coming through the firewall.

Putting an AOD or T5 successfully into these older cars can really make them much more driver friendly especially on a freeway cruise.

Hope your install was a success!