Your 1997 has either a ZF5spd or an E40D auto. Both are excellent, and adapters available for both (Advance Adpaters could help, as could High Impact) to hook a cummins to them. Early E40D's had terrible torque converters and would grenade, but the late 1990's were good. If your 1997 is an F250, that IFS front end is really nothing to brag about, could be an issue. The leafs in the front of the F250's wouldn't hold the 460 and the tires would camber out - no way without an add-a-leaf to hold the 1100# cummins. If an F350, you are set with that nice straight axle, though you may have to beef up springs, not sure.
Your repower will be quite a bit different than mine - in a good way I think. To answer your questions: My is a 1978 Crew Cab 4x4 F250. I am doing a standard (put an NV4500 5spd/NP241DLD in). If the transfer case was not available, I would have adapted the NV4500 to the NP205 with an Advance Adapters setup like Scot did in his 1978 repower talked about in this forum.
Problems mounting the motor/transmission: In the old fords, the front crossmember had to be dropped 2-3" and a body lift installed to really do this and keep clearance around the nv4500 bell housing and tunnel near the firewall, and for the oil pan of the deep 6bt to clear that crossmember. I positioned the engine where I wanted it based off other posts here, so #6 would clear the firewall and the fan would clear the stock ford 4-core radiator. Then positioned the transmission from where the egine was. I built the perches/towers for the engine by keeping the dodge factory donuts/mounts and perches from the dodge truck frame, welding them to 1/4" plate, and bolted the plate through the ford frame holes. The transmission, once positioned, was much easier - adpated the ford crossmember to the nv4500/np241dld factory mount with steel plate as well, though retained the rubber isolator parts of the mount. You might only have to move your crossmember fowards or back depending on how the cummins clears in there. Driveshaft lengths will be off now - take them to a drivetrain shop. < $100 each if you can reuse all of your parts. My front was reusable. My rear was going to be too wimpy for the cummins, so having a 4" shaft, all spicer joints/yokes, all cummins rated sizes, built. That will be $300, but I don't need the headache throwing 700lbs of torque down to the rear wheels.
I used a 1997 cummins intercooler - big, and hard to position. One from a 1991. 5-1993, or from a 1997 powerstroke, might be a better option for you. I had my radiator inlet/outlet switched to match the cummins so I could use real hoses, worked great, and not expensive to have done.
Electrical. Doing that right now. The truck runs, but jump wired. Really depends on what you are repowering with - a 12v or 24v. The 12v is easier, the 24v I don't know enough to give an opinion but lots of folks doing these too. Biggest thing here is to understand the shutoff relay and solenoid - make sure you wire the pull-in (70amp relay, power only when starter engaged) and hold-in (powered with ignition on) correctly or you will fry that pricey shutoff-solenoid. Also, wiring the alternator from the cummins into the ford will require a regulator providing field in place of the dodge computer doing that. Wiring the grid-heaters to a toggle is the way to go here as well. All in all, 12v wiring really easy, and I was fortunate to have the engine harness/underhood stuff from the donor so that helped.
Use the ford A/C pump is what I hear is the way to go. Use the Dodge powersteering/vacuum pump. Have a hydraulic hose built to go from pump to steering box, and run a vacuum line to your brakes.
Some pictures of this, and more to come some day, in my "1978 F350 Crew" project, or see my readers rigs section for photos.
thanks, jon