Personally I like the T56 and bought one to go in my caar.
The T56 has a standard 26 spline input shaft so it can use the same clutch as the TKO. Yes it is a bit heavier and quite a bit longer at about 850mm including bellhousing. This isn't a problem in an IRS equiped car though and virtually all cobras need a custom driveshaft built anyway. The bellhousing can be a problem if you are trying to mate up to an unusual engine since they have a partially integrated bellhousing. This means that part of the bellhousing is the flange on the front of the box so youcan't just bolt it up like a toploader. This make the casing of the box stronger and the load is spread over more bolts. There are factory belhousings available for quite a few motors, small block for included.
I think the mistake most people make with the T56 is the selection of rear end ratio. Yes it has a very tall 6th gear overdrive but it also has a very tall 1st and 2nd gears. 1st at 2.66, 2nd at 1.78 and 3rd at 1.3 are all taller than the TKO and much more closely spaced. The TKOII has 1st at 3.27, 2nd at 1.98 and 3rd at 1.34. The spread between 1st and 5th in a T56 is closer than 1st to 4th in a TKO. If you equip your car with a 3.9 or 4.1 rear end you will have a close ratio 5 speed with an effective 6th gear overdrive for cruising.
If you are really concerned about the torque handling capacity of the box there is a heavy duty version of the T65 rated at 550lbs-ft PN: TUET1806. Most of the others are rated at 450lbs-ft but from articles I've read there isn't much difference internally. I think it's just different synchro linings.
T56
TKO & TKOII
Cheers