Guys, I appreciate you all taking the time to weigh-in on this, but it is without a doubt caused by rollover and the noise comes from within the transmission.
There is no interference between the body and the transmission. I've checked. The trans is overfilled a bit, by about 1.5 quarts, with no change to the noise. Inspection cover was removed because it hit the ring gear (as suggested by Jrad235). I clearanced it with a heavy ball-peen and installed without issue. It's no longer hitting there.
Remember, this all started when I installed that clutch last February. The old trans sounded exactly the same as the new trans, no change there. The only thing that changed with the new trans was my ability to use 2nd gear. The noise absolutely goes away when I press the clutch, and although you can't hear in the videos, I can hear the trans internals slow down and stop making noise when I press the clutch pedal. If I slip into neutral as I roll to a stop, there is no noise until the tailshaft of the trans stops when the truck stops. If it's in motion due to the spinning driveshaft, there is no noise. 2wd/4wd doesn't matter.
It's certainly possible I have an issue with pump/injectors, but the truck runs too good for me to think that is the case, and the noise started immediately after installing the SMF clutch. I'd have to look at my records, but I don't have more than 30k on the pump or injectors I'm pretty sure.
I have less than 1000 miles on the SMF conversion, and 800 or so of that was highway miles pulling the trailer back from Albuquerque in February. Not many in-town miles to "break in" the springs in the disc of this clutch. I inspected the throwout bearing again when I installed the trans last Saturday- it's fine.
I don't mean to discard all your suggestions, but I do this for a living. I'm field technical specialist for Toyota Motor Sales. I know my way around vehicles. The reason I'm here is that everyone tells me rollover noise is normal, and I insist that my noise is NOT normal. What I can't wrap my head around is that my truck makes so much more noise than any others I've heard. I absolutely understand the role the DMF played in covering up these noises, and regret not just replacing my disc and pressure plate. Unfortunately, my old flywheel is long gone or I'd have switched back in an effort to diagnose this issue.
Ive tried 2 different single mass flywheels, and 2 different transmissions now with no change.
Merry Christmas and thanks again for all the suggestions. Ill try to provide photos as suggested by Jrad235 this afternoon.
Ryan