A built 4R100 is stronger than a built version of any transmission Chrysler ever put behind a Cummins in a Dodge pickup. Some drag racers are putting 4R100s in their Dodge trucks for the increased durability. If you plan to have your Cummins produce power beyond stock levels, even with your 4R100, i would add at least a triple disk torque converter and a valve body upgrade.
The destroked.com kit includes a transmission to engine adapter plate that will replace the one on the back of the donor engine. It will move the starter to the passenger side of the vehicle to match with your transmission. You will use a Ford 6. 0 PSD starter that will spin harder and faster than a Cummins 5. 9 or 7. 3 starter.
The kit also includes a flexplate that is about 1/4" thick, SAE rated to handle a good 1,000 hp. I've been to Scott's shop a few times and watched him make the parts. You can't get better than what he offers. If you are looking for something less expensive, PM me about some parts i have yet to get rid of.
You can get transmission controllers like the Baumannator for under $500 that don't offer a great deal of tuning but will make it shift automatically. The controller that would be my favorite choice is the PCS TCU but its about $850 with a harness. Either will give you the ability to even shift by push buttons like paddle shifters.
Without a controller, i manually shift my stock transmission shifter lever down to 1st gear to start. I have a cheap STDP toggle switch which i use to lock and unlock my torque converter manually. You may have noticed that if you take off in 2nd gear with a 4R100, it will use only 2nd gear and avoid 1st. I use this for rolling stops when i don't need quick acceleration.
3rd gear will go in via the VSS but to hold 3rd or downshift to it, you must push the button at the end of the shifter so the LED comes on saying overdrive is turned off. Push the button again to turn overdrive back on while accelerating and you will go into 4th gear.
I usually lock up in 1st gear and shift all the gears fully locked, but you have to be accelerating or the truck will buck. Downshifting with the torque converter locked will help slow the truck down much like an exhaust brake.
I can put my shifter in drive and not push the button. The transmission will shift through all four gears on its own but will not have much power in low RPMs because the torque converter will be unlocked. Allowing the torque converter to slip that much will create tremendous heat.
My dad was driving this truck first without the torque converter lockup switch. Transmission temperature went over 238 degrees and the truck would barely hold 60 mph up hills. Now my transmission is often barely over 104 degrees while cruising and i can leave about 60 feet of rubber marks on the pavement when i do burnout.
Your transmission controller will need inputs. Not sure if the V-10 has a MAP sensor, but that would make a good digital load input. You'll need a TPS signal, RPMs would be good too. VSS and brakes are other typical inputs as well. Your speedometer will still work but other gauges may need modifications. Cruise control and throttle cables should be fairly easy to hook up.
You didn't mention if your truck is 4 wheel drive, but not only is the 4R100 stronger, you'll also want to stick with the NVG 271 or electronic 273 that comes stock in the Ford as it is the strongest factory transfer case available, i think even today.
This should give you enough information to mull over for now but if you have more questions, don't hesitate to ask.