Unfortunately good manual gearbox options are not as simple as automatic and much more expensive, but its worth it :-)
I had a Muncie that I made fit in the standard tunnel using modified Hurst shifter and custom linkages (necessary if you want a console), I reckon its not a bad option to go with one of those new heavy-duty boxes if you don't mind a four speed. They can be made to shift very nicely and a lot of fun to drive.
http://www.gmh-toran...e-8#entry725344
I don't see how the Supra box would fit properly without at least a little cutting, even the W58 needed a bit of extra around the shifter and forward a little if you want decent driveline angles. To me trying to fit anything bigger without cutting is just shooting yourself in the foot as you're trading one problem for another, I'd rather have it done right (watch out for bolt-in 'kits' that don't require cutting). You also need to allow for bigger driveshaft yoke even with the 32 spline Muncie, the five and six speeds are worse as they are longer and move it further rearward.
Some people get away with T5s but I wouldn't spend money on one as its lifespan is more likely to be short, little better than the W58.
Hydraulic clutch release works great with the throwout bearing type. The clutch itself depends on how you drive the car and how often. I had a few different heavy duty single plate setups and the only one that lasted long was ceramic button on the pressure plate side but it was worn out in under 24 months which apparently is normal. Now have a twin plate full organic setup which seems to work well and should last longer but price is not "reasonable".
Ceramic clutch damage, hydraulic throwout, also scroll down to see tunnel cutting for TKO:
http://www.gmh-toran...-11#entry900805
Twin plate clutch:
http://www.gmh-toran...15#entry1027214
I'm reasonably happy with the TKO600 now things are pretty sorted but it didn't fit easily, in hindsight I'd probably just take the simpler route and go T56/6060.
Also have the 28 spline Borg Warner with factory R31 axles and Tru-trac. Only behind a mild 355 but they survive this sort of thing:
Well, sort-of. Both axles are showing a bit of twist at the spline end so no more of that for now. Kind of invested in the 28 spline now since the centre was so pricey, in hindsight I'd go straight to 31 spline but I'm thinking some decent custom axles in 28 should be enough to solve the problem.