727 transmission or 340 trans

you are over thinking it. generally, if you are over 450HP you dont want to run the stock 4speed, you will tear it up. so if you prefer manual and go higher in power think T56, g force, lenco, etc.

as far as automatics... a 904 or a 727 will get the job done... if they are built right. a lot of people just stick with one or the other if that is what came in the car, so they dont have to mess with changing driveshafts etc. CRT is a place where a lot of people get theirs rebuilt, John Cope has a great reputation on several web boards. he and many others recommend PTC for torque converters. just call them after you know what HP goal you have and what cam shaft / trans you are running if you go automatic.

in any event, you might want to put new universal joints in while you are upgrading. if you are going super high horsepower/torque you might want to switch to 1350 series joints.

good luck!