trans swap
Hummin Cummins:
I did the swap you are contemplating one year ago.
In addition to all the advice given so far, I will offer some observations.
Gauge cluster: the gear position indicator can be removed easily and swapped into the manual gauge cluster and vice-versa, if you want to keep your odometer reading accurate.
Wiring harnesses: There are many differneces between the two under the hood, but under the dash, the plugs for the O. D. cancel switch is there on the manual truck also, taped back to the harness, and the Trans temp light is there in the manual gauge cluster also.
I did my switch by buying a '94 BR2500 with a 5 speed to use as a donor for the auto in my '94 BR3500. I bought it cheap enough to do the swap and resell the 2500 for what I originally paid, but liked the truck enough to keep it for the daily driver. There is a difference between the transfer cases. The 2500 t-case has a tag that says NV241 DLD (Dodge Light Duty, I suspect), and does not have a p. t. o opening. The 3500 has a t-case tag that says NV241 DHD (Dodge Heavy Duty, I assume) and has a p. t. o. cover. The input shafts are different between the two, as is the overall length which makes me think the chain in the DHD is probably wider. The crossmembers are the same, but the transmission mounts are slightly different. Because of the length difference, I swapped driveshafts (Front and Rear) between trucks and they bolted right up to the pinion flange, and I believe that the 2500 had a Dana 70. Engine wiring harness AND COMPUTER were also pretty easy swaps.
I was able to swap the carpets between trucks also because they both had the same interior color. There are a couple of fittings on the block that needed to be swapped out for the transmission oil to water cooler, and it was relativly easy to swap the clutch pedal from the 2500 to the 3500. I believe that buying a complete truck and reselling after the swap is the cheapest in the end, and you are sure to have ALL the parts you need. Think of all the little parts you need, like cooler line clamps and brackets, both the oil to air and oil to coolant heat exchangers, shift boots ect. that go into the swap. When I was done no one was able to tell either of the trucks had a sex change. An added bonus was that I got to drive the donor transmission around for a month to prove it was in good working order before the swap.
My opinion was that the manual if fine for towing, but brings a little more noise into the cab thru the gear shift, and it sucks to drag race all those little Jap imports now because of the turbo lag between shifts. I have ridden in a couple of trucks pulling trailers that have installed ATS triple loc convertors and well-built trannies and would probably go that route if I had it to do over (triple loc wasn't available when I did my swap). Drag racing is far more satisfying with an auto, also. Those convertors really work great and prove that the transmission isn't really the weak link that most people think it is. I say this and want you to know that the primary use of my 3500 is to pull a gooseneck that puts GCWR at about 20,000#. But hey, I understand that some people prefer a stick, plain and simple.
Good luck whatever you decide, and I hope I have provided some useful info.
Attention: TDR Forum Junkies 
I didnt want an auto to start with, but for the $ I paid for mine, I couldn't pass it up. 
Spent a lot of $ this week and I think she's in shock. I'll try to present it when she's on a better mood.
I've done a few swaps but the donor cars were really dead, as in totalled.
