It's really tough to try to diagnose through the internet without actually seeing the truck, but with what you have done so far I am wondering about a couple of other areas that your recent post indicates should be looked at.
P0478 and P0470 have to do with the Exhaust Backpressure Valve. Has anyone removed the EBPV sensor (front passenger side of engine) and the tube between it and the manifold? It will get plugged with soot or actually get a hole in the tube causing the EBPV to close. If that happens, you will feel as if the engine looses all power due to a loss of boost. I have also heard of cases where the EBPV will simply stick in the closed position due to carbon build-up. If this were the case, you should be hearing a loud hiss coming from the engine and exhaust while running tho.....
I also wonder about the fuel system itself....pump and potential areas of the pre-pump fuel lines that are susceptible to air infiltration. scott had mentioned this in an earlier post. If you are leaking a lot of air into the suction side of the pump, the engine will dramatically loose power, usually while trying to work hard. A fuel pressure guage mounted to the fuel bowl will show if you are loosing pressure to the fuel rails that would cause these symptoms including injector knock (air in fuel). In-tank modifications along with pre-pump fuel line modifications (known as the Hutch Mod) will eliminate these problems but will also require the installation of an aftermarket fuel filter (pre-pump filter). On another forum, had a mechanic with a customer complaining of similar conditions and was advised to do the same mod with a kit from ITP Diesel and cured the no-power complaints of his customer. It would be worth watching what the fuel pressure does while running rough to determine if this is a potential problem.
