The LAST thing I'd try to run would be the 6.7 ECM, simpler in most cases is better.
That having been said, Pete's right, if they'd tried to do a viable DPF system in the '90s, it would have been an outlandish clusterduck of wiring, hoses and modules up the ying-yang.

Sad thing is, the only thing that's going to stand a snowball's chance of keeping up with the EPA, is computer technology.

If you must have EFI Live and you want tune-ability, the '06-'07 5.9 system is tune-able via EFI Live, plus you can do away with the VGT and run something of real value for a turbo, if not a compound set-up.
If EFI LIVE isn't in the cards, then hands down, the DUMBEST Commonrail system you can run is an '03-early '04 manual trans ECM and wiring, preferably from an HO application, then add a programmer.
I kinda' like the idea of the '06-'07 5.9 ECU and harness, because, stupid of a reason as it might seem, if you put it into an older vehicle, the APPS isn't a PITA to work out.
Just mount the pedal to the floor where you like it, run the wiring to it and DONE, no figuring out APPS cables or routing and mounting places that a cable will handle.
In truth, the SIMPLICITY of the EFI on a commonrail is what makes me hesitate on continuing with a mechanical version. Mechanical DOES rule from a simple and "fixable alongside the road" standpoint, but there's nothing bad to be said for that extra kick at the flip of a switch, either.
Mark.