I put a T5 in my '66. Although, I did a 5.0 conversion, so I just kept everything true to it's Foxbody-roots. I used a modern-driveline cable clutch, but if I were to do it again, it would likely be a McLeod Hydraulic clutch. The crossmember is easily found. I had to 'modify' mine just a tad with an angle grinder, but it was no huge deal.
The fit should be fine though, unless you use an aftermarket shifter. Before I killed my original T5, I had no shifter-hole fitment issues with the stock shifter. When I put in the T5z, I had to open up the shifter-hole so that my Pro-5.0 shifter could fit.
Your driveshaft will likely need to be modified in length, and will also need a different yoke (IIRC).
I definitely enjoy having a 5-speed in a car that never came equipped with them. People's reaction to seeing a 5 speed shift ball are pretty great. Rowing the gears is fun too. It will definitely pep-up your acceleration and/or mpg's, as well (you can only pick one, there, hahaha)
66 Coupe- 5.0 EFI, T5, 8.8, 4-wheel-discs, blahblahblah
Carolina Crew #82