Hi Bomber,
Ditto on the Lugnutz comment. Great guy and very helpful. The T5 and 12 bolt change worked out great for me. What I did was to figure out which of the T5 gear ratios when combined with my 3.07 rear end would produce as close to the same overall ratios as the AD truck had when it was brand new. After that, it was a matter of making sure my 5th speed was .86. Anything less than .86 with a 3.07 rear wasn't going to do anything but lug the engine. Plus I now have a fully synchronized transmission, 4th gear is a 25% reduction from 4.11 and then 5th is about 2.66.
The bottom line on the 12 bolt swap was this:
you need a driveshaft. I had mine made by a place in San Antonio and it was about $400. If you can find a used one it will be less expensive, but the wrecking yards in DFW have turned into slumdog apartments.
if possible, get the emergency brake cables with your 12 bolt. You can adapt them to work with the AD setup.
you will cut off the mounting pads on the axle. You can use a cutting torch, but be careful not to get one side of the axle tube too hot. Do it in bits.
your work will be easier if you use adjustable (bolt-on) spring perches and then weld them when your pinion angle is set.
the other brakes are simply a matter of making sure you can connect your flex cable. BIG TIME HINT: keep the hookup (tubes and 3 way connector) from your torque tube rear. It can easily be adapted to the 12 bolt.
shocks...you will need a drill press but you can convert your AD shock mounts to work neatly with the 12 bolt and use the same shocks.
brakes...shockingly similar to the 52 and newer AD type.
Back to the T5, get one of the gizmos out there to raise the shift lever up and shorten the throw. They aren't costly and there are two kinds...one is 1 inch thick and the other is 1.35" thick. The guy who makes the 1.25" thick one is a real gentleman. When you get to this point, contact me and I'll give you his info. IF you can't find one with a mechanical speedo output, don't worry. It isn't difficult to make an electronic (or GPS) speedo look very much like the original. Will it bolt to the 216 bell housing? I think the 48 and up truck 216 bell housings used the same bolt pattern as the T5 but let's see what others say. It works fine with the 235 bell housing. You will need to fiddle with the throwout bearing and use a clutch disk that fits with the T5. Not a problem. Plus you get a reverse light switch with the T5. Nice to have.
The 3 speed with the closed driveshaft will only work with a closed driveshaft. Completely different design, but you can rebuild it, install the 3.55 rear end gears and cut 14% off of your highway rpms. Note: your take-off gear ratio (some call it the starting line ratio) will be reduced to 10.4, so you won't be able to haul 1000 pounds of stuff in the bed as handily as with the stock ratio, but not everybody cares about that. If you hark back to my starting comment, it was important to me that mine still operated just like a stock AD pickup, however. Hope this long winded comment helps. Good luck.