Charlie suggestion is a good one, Chris. The T-5Z has a lot to be said for it. What follows is a small piece of what is presented on the Modern Driveline web site in the 'Tech Alley' section labelled 'T-5 History'
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The "Z" Spec T-5 "In 1993 Ford started offering a new service unit to the Ford Motorsport crowd. The nick name T-5z comes from Ford’s part number, 7003Z. This Ford Motorsport T-5 is also sometimes referred to as "World Class T-5". While it is a Word Class T-5, as it has all the upgrades, having a 2.95 first and “Cobra pocket bearing does not make it “World Class”. The T-5z is a 1993 Cobra T-5 with 2.95 first gear set and .63 over drive. It has the best of everything. Hardened gears, short throw factory shifter, steel front bearing retainer, and tapered output shaft bearing and a seven tooth drive speedometer gear. Best of all it has a torque rating of 330ft/lbs. based on 100,000 mile usage. The stock T-5Z can handle up to 450hp with a soft locking clutch and is not shock loaded like in drag racing."
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NOTE: The T-5Z 5 speed transmission weighs only 75 pounds! Also, IF you look at the Modern Driveline web site, you'll see that they also offer the option of a .73 overdrive ratio or a .59 overdrive overdrive for an additional charge. The .63 5th gear overdrive ratio is the standard TREMEC offering.
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I think well of the Borg Warner T-85 three speeds with overdrive. However, T-85s do not have a synchronized first gear, weigh in at just about 150 pounds, and have been out of production since the early '70s. They are rugged. My recollector is that Ford used them not only behind the y-block 312s, but also behind the FE 352s, 390s and 406s.
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Other ways to go IF you are not looking for an overdrive gear to reduce highway rpms, engine wear, and gas usage:
1) In the sixties Ford offered a 3 speed all syncro transmission. Those that have mentioned it in other Forum threads have, I recall, stated that it was top-loader design, rugged, and that its synchronized first gear added to its drive-ability.
2) Borg-Warner T-10s (I'm hearing parts are getting tougher to locate for these, just like the T-85s)
3) Ford top-loader four speeds
I'm sure others will chime in on this for you. 
NoShortcuts
a.k.a. Charlie Brown
near Syracuse, New York