Agreed, the 05+ transmissions cost a little more, and need a speedcal, but physically bolt right in. Just take the PRND21 template out, fab up a boot (I believe the C5 Corvette boot works well) and row those gears.
I've been working on the math, and the MT82 doesn't go well with short gears. First gear is very short, 3.66:1 and second is 2.43:1 If I had 3:55's or 3.31:1 rear gears, it'd be a great transmission, but with my 3.73's I'd have to shift all the way to third to get up to 60mph!
The T56Magnum however, while more expensive, has a 2.66:1 first, and 1.78 second, so I'd be at 49mph at 6500RPM with the T56, vs 31mph (and there VERY quickly) with the MT82. It'd be a great corner carving transmission with taller gears, but I don't want to row all the way to 3rd, or change out the rear gears either. Plus with the T56 Magnum having mechanical pickups, I should be able to not have to fuss with a speedcal.
I guess it depends on your grand plans, these are revvy motors with shitty low end, and a 2.66 first is even lower than the factory 4R70w 2.84, bleh. T56 ratios work better in conjunction with a lazy large displacement engines or ones with a positive displacement supercharger, which is why Ford used it on the 03 Cobra(not strength as commonly believed, the T56 is about as strong as the T45). I wouldn't even consider using a T56 on a NA/centri 4.6
As for the speedcal, the adjustability is quite nice. I know you've mentioned your tire selection being based on speedo accuracy numerous times but with the speedcal you can use whatever you want without worry, just do the math and set the switches.