I'd say for good performance and the ability to still be used as a daily driver, I would look at the following things:
Exhaust:
Headers (dual outlet)
dual exhaust (2" - 2 1/2")
Performance muffler(s) (flowmasters, etc.)
Ignition:
HP ignition coil (40,000 volt Pertronix Flame thrower or other)
Electronic ignition (pertronix breakerless ignition system)
Distributer (lots of different ones used by all of these guys)
Tranny:
The T-5 you are talking about sounds great - will provide a lot better gears
Engine:
Performance rebuild (if needed) - (push rods, valve springs, rings, etc. etc)
Mill and deck the head
(possibly a performance head - aussie or other - lots of help here on that)
bigger valves (intake, etc)
3 angle valve job
hardened seats (for unleaded gasoline)
A good 2 or 4 bbl carb (Weber or Holly)
There is a LOT of great experts on here to talk to, and a lot of really nice sites to pool idead from, feel free to check out mine to get some ideas, and to see some of these things I just mentioned.
www.geocities.com/levidodd7/65stang