TSielski--
I didn't have the good folks from anywhere do my transmission swap (which is not 100% complete because the auto is still out for rebuild).

What I learned from doing it myself is that, hands down, it is much easier to have a complete donor vehicle. It would be easier to switch from the auto to a stick, but much harder to switch the other way. I elected to purchace another truck (hey, if one Cummins is good, two is better!) to do my swap.
I wanted a 5sp in my '94 Dually, so I located a used '94 3/4 ton with a stick. Here's what had to be swapped to the DUALLY to convert it to a STICK:
1) transfer case (input shaft splines are different)
2) driveshafts (mine are both 4x4, same wheelbase, but trans/transfer length is different)
3) plug water to trans oil cooler coolant lines, remove both coolers and lines (do you realize the air to oil cooler can't be removed unless the front bumper is removed?)
4) swap engine compartment powertrain wiring harnesses
NOTE: the wiring for the auto transmission does not exist in the stick harness, so a swap TO the stick would not require step 3 & 4, but I needed these for the other truck.
5) Swap steering column and clutch/brake pedal bracket (also remove the gear position indicator from instrument cluster)
6) (for stick) install clutch master and slave cylinder and resevoir.
7)(for stick) cut floorpan to acomadate gearshift lever, aquire shift boots. I swapped carpets and had to fill in the hole on the other truck to put the auto in.
8) remove jumper from harness and plug into the Clutch Safety Switch.
9) remove TPS and mount from throttle linkage, also T. V. cable (for stick) (add for auto)
There is much more to do if you want the conversion to look truly "clean". My main point is that I was stunned by all the "little things" I never thought about needing when I was considering just buying the parts for the conversion. My advice is to buy a donor vehicle of the same model year and swap trannies between the two, then resell the donor as an automatic. The amount you lose in the resell would most likely be less than buying all the parts outright. (the shift boot assembly, which is 2 pieces, alone will cost over $120. 00). Driveshaft lengthening and rebalancing (2 shafts if 4x4) will run a couple hundred. Do you need to buy a clutch? pressure plate? bellhousing? Gearshift lever? It may well be cheaper to sell your truck and buy a different one.
Having said all that, I can tell you I was stunned by the performance improvement the stick gave me in the dually (249 hp / 615 lbs-ft on the dyno). I never realized how much power that torque converter uses up to heat up that transmission fluid.
Research your options and costs carefully and if you decide to go ahead plan for 30-50 hours of work if you do it yourself. Drop me a line if you have any questions & I'll help you out if I can. Good Luck!