Okay. I own a few different turbocharged vehicles, most of which are these trucks with a turbo on them. I also own a 97 turbo Eclipse, and I can tell you any stock mitsubishi turbo will not suffice. They are far too small.
The T04E Garrett cartridge is perfect for these trucks, and you cant deny allot of thought was put into the selection of turbine and compressor that was used to compliment these engines. Too small of a turbo and you're wasting your time and money, to large and you're in the same boat. Allot of people think just because a turbo is BIG it will make your engine run better, that is not true, if you get to big of a turbo it will lag and spool up time will be far up in the RPM band. Such as the case with a power stroke turbo, I realize it will boost, but you will not receive optimum efficiency out of your engine with that large of turbo. Another way of putting it is, a power stroke turbo will lag like an old lady crossing the street.
To be honest there is no better turbo for these trucks than a T4 size turbo, and really there is only one thing that could be done to the T04E turbo to make it produce more and that would be to have a custom ball bearing cartridge made.
If you insist on building your own kit the T4 is definitely the way to go, the exhaust inlet flange is a common one and is easy to get an up pipe for, and I would stick with a V-band style exhaust outlet as that is also easy to get an exhaust shop to make a down pipe for.
I would suggest finding a rebuilt factory wastegated turbo or the like. Talk to Typ4 he may have one.
I have my old cartridge that I will be trading him for some stuff, and if he can find the housings he can build something that works for you.
Otherwise I will keep my eye out for what looks like a good subject for you.