This isn't a direct answer to your question, but it might help. Back in the '70s, we converted several '61-'63 T-Birds to stick shift for circle track racing. One 4 speed we used came from a '66 big block Galaxie. Other than the tranny mount being different, it fell into place with no driveshaft alterations and we used the T-Bird yoke plus rear U-Joint. So that would lead me to believe, but not with 100% certainty, that the '65-? fullsized Ford FMX or C6 has the same overall length as the MX originally in your 'Bird. That'll at least give you some measuring options.

As to whether the FMX or C6 is better, it depends on what you're planning for your 'Bird. FMX's are tough enough trannys, but expensive to have rebuilt and there's not much performance support. Were I planning to build a strong FE, I'd definitely go with the C6. They eat more horsepower than an FMX, but are arguably stronger and you can buy shift kits, stall converters and such about anywhere.

Jan