I would go for one with the shifter in the right spot, and deal with the other specifics.
Not saying it would be like this, but I saw an old AMX with a 6 spd swap, and the shifter was the ugliest thing you ever saw. It had a big 90 deg turn towards the front. It needed a console to hide all that shit.
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.
97 Thunderbird LX (The GT Bird)
2003 Explorer WAP block with Modular Head Shop "street ported" heads and Stage 2 PI NA cams, 75mm Accufab throttle body, C&L upper intake plenum, Kooks 1.75" primary/3" collector headers, 2.5" full exhaust with mid mount Magnaflow dual in/out muffler, 24lb/hr injectors, 80mm MAF, Tuning from Don @ www.lasotaracing.com
, CAI that feeds from fenderwell. Jmod, 3.73:1 TL in Mark VIII carrier, Mark VIII aluminum LCAs, 93 Mark VIII driveshaft, PBR brakes (soon to be Cobras), 18x9 wheels with 35mm offset, 255/40/ZR18 Tires, Front and Rear strut/shock bracing, GR-2 shocks, Eibach 1.5" springs, 1989 SC front and rear sway bars.