Nick,
I got my TKO 600 as a complete package from Mike at Forte's Parts Connection Forte's Parts Connection - TREMEC, FACTORY FIVE COBRA PARTS, FORD RACING PARTS, FFR, MUSTANG, TRANSMISSIONS, T-56, T-5, TKO, TR-3550 After hearing about him here on CHR I sent him a message, we talked about what fit my build, and I ended up buying a complete package from him - Tremec cast bellhousing w/dowels, flywheel, clutch, hydraulic slave, and starter along with the tranny. My clutch is a Valeo single disc, I've never had a problem with it holding the torque and the pedal pressure is low - no difficulty actuating it at all. The Valeo Valeo Clutches » Products » Clutch Kits » Performance Clutch Kits :: Performance Clutches :: Valeo Clutches is used a lot in the Cobra packages, including their race applications, and you'll see lots of discussion about them in the Mustang forums, too.

On the 5spd vs 6spd, the big difference in my mind is that the 6spd gives you two overdrive gears, on top of kicking you up to 700ftlbs of torque capacity. You have two different gear ratio selections to choose from, one with 5th at 0.74 and 6th at 0.50; or with 5th at 0.80 and 6th at 0.63. The selection of your transmission needs to account for all of the variables - your engine torque curve (rpm where you're well up on your curve is critical), rear gears and tire diameter all interact for a good selection. I can tell you from my experience my 0.64 final drive puts me just below 2000rpm at 70mph, and the 0.50 would drop me down to 1560rpm which is a bit low for me. If I were running a T56 6spd I'd be on 4.56 rear gears, or even another notch lower which just doesn't make sense for an around town/cruise car in my mind.

If you get ready to jump into a stick and decide to go with a new tranny vs salvage I'd advise you give Mike Forte a call, explain what you've got to him (engine, approximate HP & torque, rear gear ratio, rear tire diameter), and let him chew on it for a few minutes to come up with a recommendation. You will not be disappointed with Mike - he's a great guy, and he still remembers me (Roger from the KC area) any time I call him.