Did you ever make a decision on this? I would certainly keep the CTA motor and build it to your needs. Absolutely no reason to swap it out, certainly not with a Big Cam Cummins. The 8.3 can EASILY make 450-500 hp and 600-700 is not a stretch at all. Call some shops like Scheid Diesel, Garmons, TST, etc. Any of the big sled pulling or drag racing shops should be able to tell you exactly what you need. The mechanical motors are bulletproof and will run on almost anything. Many of the military CTA's have the MW pump instead of the Bosch P7100, so keep that in mind.
An SAE#2 bellhousing should give you a ton of options for both manual and automatic transmissions. A company like Suncoast could probably build an Allison automatic (2000/2500 series) to handle 1450-1850 pounds of torque, but you might not want to pay the bill on that build. ($10 -15k is my guess) not sure how that compares to some of the other options mentioned.
If you dont mind rowing your own gears, get an Eaton Fuller manual and throw a good heavy duty clutch in it and you are just about set as long as you dont go stomping on the gas in first gear. Many new auto trans for the higher HP truck motors are limited to working with the engine and only allowing a certain amount of torque until the RPM and/or MPH come up to acceptable levels.
If you insist on swapping the motor, I would only consider building a mechanical DT466. You should be able to get 550-600 hp out of it very easily with a call to a shop like Hypermax Engineering or Gene's Garage. Very popular in the tractor pulling world with several in the 2500 - 3000 HP range on several hundred pounds of boost. Not sure what they are doing for transmissions to hold that kind of power, but it comes on at much higher RPM, therefore you lose the large TQ to HP gap common in larger diesel engines.