I just noticed your question - and since I have done this conversion on a 64 Fairlane, I can offer the following.
About 22 years ago, I replaced the 260 engine with a 65 289 (6 bolt). I used a bell housing adapter from Advance Adapters in order to keep the original 3 sp manual with overdrive.
6 years ago, I replaced the overdrive with a non world class T5. I used an adapter plate behind the 65 bell housing. Even though the transmission is located about 5/8 further to the rear, I was able to retain the original crossmember (has slots). About 1/2 inch of shims were added to lower the rear part of the transmission in order to avoid hitting the floorpan. I was able to retain the original drive shaft without cutting. The original yoke was replaced with the T-5 yoke.
I am about 5'9" and I normally adjust the bench seat about 2/3's of the way toward the rear. The shifting tower of the transmission is located just forward of the seat (just clearing the seat). I had to turn the gear shift lever backwards to complete the installation. Sometimes in the future, i will need to have a custom shift lever manufactured to avoid "reaching".
With this arrangement, short drivers will not be able to reach the pedals as the seat cannot be pulled forward. My opinion is you need a 3.5 rear axle ratio - or lower ratio - to prevent lugging the engine in 5th gear. You might discuss this with modern drive train. The T5 gearbox is as smooth as they come. The .63 overdrive ratio is a little tall. I would have preferred a .68 ratio or a custom ratio around .75.
Larry | 
