So...Since I have to part ways with my rig, I thought I'd tie this thread up a bit and let any people with similar problems as to mine know what was eventually found.
Leaving the country and running out of time, I decided to leave my rig in the capable hands of Torfab. They systematically went through and narrowed it down. Compression test: Perfect 475's across. Pulled the fuel injectors (again) and had them tested: All tested great. Re-installed the injectors and still no change to the rhythmic sound I had and a lack of power. Pulled the injector pump and had it looked at. Needed a rebuild badly. Done. Reinstalled it, no change.
And then they started moving the injectors around (Well, I may have the order of operations slightly off here so give them the benefit of the doubt). What they found was the misfire followed two injectors and that they had no soot on them after running. And yet, they all pop tested fine. They had some extra injectors laying around from another project and dropped them in the place of those two. Low and behold, she ran perfect! So even though they were supposedly in perfect shape, they weren't working correctly. I'm not sure what the lesson is here, but if you get the same sound and symptoms as I had, start with moving the injectors around. Best of luck!