Sounds alot like my 2003 250HPDI...ended up being a blown engine (one cylinder lost compression, but was still running, but not great). Got new powerhead (and all maintenance items including plugs) replaced under warranty no cost to me, except a new larger battery. See my thread "250 HPDI knocking noise" for more details.

Is yours still under warranty? Hope it's something simple like an injector or fouled plug! Good luck!
Mark