With regard to the engine...
Here's my take on it, for whatever it's worth.
Klenger - don't be so quick to point out no lift pump problems on the 3rd gens. There've been quite a few around here with failed lift pumps, some of which took out the injector pump.
On the one hand, the CP-3 is a very simple pump. It only has to pressurize the rail, so there's no need to "time" the pump like on a VP-44 or P7100. That should make pump replacement easier. On the other hand, it's a very very close-tolerance pump with very high pressures which makes it ultra-sensitive to contaminants in the fuel. Not to mention the problems with containing fuel at 1600 bar safely.
The injectors in the common rail engine are still "up in the air" as far as I'm concerned. There's a lot of trucks with failed injectors. At their core, they're a very simple design. But like the CP-3 they're very high-precision and contain a very small check ball that seems to be somewhat troublesome (injector stick-open issues).
In my opinion, the fuel system is the "weak link" in the common rail engine. There are too many precision parts, and rather high pressures at work. The remainder of the engine is excellent, with a significantly stiffer block, better piston cooling, and more electronic controls (I think electronics are preferrable - like distributorless ignition systems).
You mention that you're going to bomb the truck. It *appears* that bombed 3rd gen engines have notably shortened lifespans, so if bombing and long life are what you desire you might choose an older engine. 12v guys seem to be able to bomb the you-know-what out of their engines with little or no bad consequences.
I should note that I never owned a 12v or a VP-44 truck.
-Ryan
Disclaimer: I am not being mean spirited or rude in any way to anyone who owns any truck or vehicle. I am not bad mouthing any person or group of people. The information in this post is pure opinion, and I make no claims to it's basis in fact or reality. I encourage everyone to conduct their own research and reach their own conclusions.