Engine knock

While pulling a heavy RV out to West Texas this past weekend my 01 2500 diesel developed a knocking noise. It's most noticeable on the drivers side and on the inside of the cab. It follows the RPM. There was no change in performance, oil pressure or any other engine parameters that I could tell. I used a mechanics stethoscope over just about every square inch of that engine and nothing seems out of sorts. I pulled a couple inspection covers off of the transmission and noticed that at least two of my bolts holding the flexplate had backed out slightly, I tightened them but the noise didn't change. I cut open my oil filter and noticed a few, what looks like metal flakes but they are not magnetic. I'm leaning toward a cracked flexplate but I want to investigate everything before I have to drop the transmission. Has anyone had a similar experience?

let's hope that it's just a flex plate. The only time I heard a cracked flex plate was on a 59 Chev. I thought it sounded more like a popping noise, rather than a knocking noise.
As for the metal particles in the oil filter, could they be pieces of the rod bearing material?