That motor responds to mods much the way the smaller B (5.9) engines do. To get a good power increase while maintaining drive-ability and reliability (in almost any diesel) you need to look at only three or four things:
Getting plenty of air into the engine - factory intakes, air filters and heads are usually less than ideal. How much work you do here depends on budget and can be as simple as a Big Honkin' Air Filter. (google BHAF) Another option would be larger intake tubes or smoother/cleaner path of existing tubes, though this is not a huge issue for mild power increases. Turbo piping and couplings can also be an issue.
Getting the right amount of fuel for the amount of power you desire - you dont want clouds of black smoke belching out the exhaust but you want more fuel than stock. Most pumps are VERY conservatively tuned in stock form. Several threads on here about simply turning up the fuel in a muti engine and how much difference that makes. With the CTA motor, you most likely have one of the baddest a$$ pumps on the planet - the Bosch P7100. It can be built to support over 1000hp on a B Series Cummins. Everything from grinding the fuel plate (free) to buying a modified one (pretty cheap) to full custom pump builds ($$$) is available. Any reputable diesel shop should be able to do this for you and there is plenty of info on line for DIYers (diesel forums, magazines, etc) Injectors are probably a bit further down the list, but they are not terribly expensive either if you wanted to move up to that later.
Next and probably last is exhaust. Again, not a huge deal for mild power, but unlike gassers, diesels really dont need or use backpressure. The idea is to get rid of spent exhaust gasses as quickly and efficiently as possible. Make sure your exhaust system (including all turbo parts) are in good condition, nothing loose, worn or out of spec). If you want to go to a larger exhaust, it can be a cheap way to free up some horses, in conjunction with the mods above.
With any mods on a diesel you need to monitor EGT or exhaust gas temp and trans temp if you have an auto. This will tell you what your engine is doing in the power department. If you dont have an intercooler or your cooling system is not adequate for your new power level EGT will quickly get out of control. Adding an intercooler can be another way (can be done on the cheap) to free up HP. For Tems: Post turbo you want to stay around 900 - 1000 degrees and pre turbo you want to stay under 1300-1400, though short burst to 1500-1600 should not do any damage.
The article linked below for the 12 valve B Cummins (one budget on each page) will give you some ideas for your CTA.
http://www.dieselpowermag.com/tech/dodge/1002dp_1994_to_1998_dodge_ram_power_recipes/index.html
On another note, i was not implying that 400hp/1200TQ was difficult or expensive to achieve from a CTA. In fact I would say the exact opposite, those numbers should be pretty easy to achieve. If you really wanted BIG power out of a CTA motor and had the budget 1500-2000hp would not be out of the question, but that is not for discussion here.
EDIT: Brakes and driveline are mentioned below, so I am editing this instead of posting again. Much of what comes out of discussions like this is info taken from other activities (rock crawling, drag racing, sled pulling, one ton show trucks, whatever) Turning up a CTA or building stronger axles is not specific to military trucks. Yes you should have adequate brakes to stop your truck regardless of how much power you have. If the stock brakes are not adequate (and they probably arent), then upgrade. Several companies offer disc kits for 2.5 tons, threads abound on DIY disc conversions and there is a recent thread here about 5 ton disc conversions.
This thread is about the differences between the two motors, not brakes or driveline. I have seem stock 16 splines (2.5t) break pretty easily rock crawling (old and brittle, not too much HP). I have also seen 600-800hp rock buggies on 44-49" tires beat the $hit out of built 2.5t axles and not break them. If you are breaking axles, transmissions or transfer cases in mildly turned up 5 ton driveline, your problems are not from a few extra ponies in your Cummins motor, regardless of which one you have.
As with any vehicle, know the condition and the limits of your rig whether you are doing a parade, drag racing or rock crawling.
Hope that helps.
Cheers,