Also, I went back and read all the posts from the beginning.
Your comment about the marks on the cam gears lining up is likely to mean you haven't read through instructions on how to time the engine? No criticism, only to point out that the marks mean nothing... so you cannot conclude that the engine is in time based upon those marks (the ones stamped into the gears). Also, if you adjusted the timing *at all* based upon them, you are likely off enough to have broken the rocker arms on one or more cylinders - thinking that was already the case tho.
Looking at the codes - many can be set aside for the moment with diagnostic efforts as the probable cause; here I'd cite your post regarding disconnecting fuel while running / diagnostics, pulling the MAF sensor, etc. The MAP code is expected with the turbo / CAC hoses disconnected since no boost is making it to the intake; the computer wonders why... again, expected and not the cause of the rough running.
I agree with the post about P0610 - sounds like the computer (ECM) is needing to be reset using a DRBIII or possibly re-programmed by someone like GDE. I don't think that's the cause of rough running at the moment. Here's one reference re: P0610
http://www.jeepforum.com/forum/f28/06-crd-obdii-engine-light-code-p0610-664875/All the above and the appearance of oily back-flow coming out the FCV lead me to believe that the timing belt has jumped or is out of alignment and that one or more cylinders isn't getting it's valves open/closed any more (or, perhaps partly).
Since you've pulled it apart as far as you have, I'd plan on getting the tools (rent from GDE) and pull the engine cover to inspect the rocker arms. That will tell you how much work is left to do? While you're doing that and perhaps waiting for parts - if you can get the ECM to GDE that'll be one problem out of the way.
Wish I could offer better news - but I can relate... Your's may have jumped at 140k, mine did so at 145k. Actually, once I got the belt off I could see the teeth on the belt that had snapped off.
Mark