Sorry to bring this back from the dead, but did you ever figure out a fix for the rattle? I have the exact same rattle (video link at the end), and am wondering how you dealt with it.
I've always this rattle/grind at low RPM that sounds like the engine pulses are causing the gear teeth to bounce off each other. Its the most obvious with the transfer case in neutral and the trans in gear (no excess road/engine noise), which I thought was bad input or countershaft bearings in the trans or a worn out coupler/mainshaft.
I pulled all the gearboxes (ranger torque splitter, 465, 205) and rebuilt them. The bearings looked fine but I replaced them anyway due to age, and I got a new 10 spline mainshaft in the 465 and a new coupler sleeve to address some significant spline wear.
I have everything back in the truck. Bellhousing aligned, new flywheel and clutch, new pilot bushing, throwout bearing correctly installed, new bearings in all gearboxes. And I still have the same noise.
The following video starts with everything in neutral and the clutch engaged and there is no noise. So this seems to rule out anything to do with the clutch. At 0:09 I disengage the clutch (still no noise), put the Ranger (2 speed transmission in front of the 465) in gear and let out the clutch, and I get a low growling noise as soon as the clutch engages and the SM465 input shaft starts to spin. Up to 0:15 I put the clutch in and out a few times and you can hear the stop as the clutch disengages and then immediately resume when I reengage the clutch. Then I put the trans into second, then third, then the Ranger into overdrive and the rattle gets louder with increasing output shaft RPM. At the very end I rev the engine slightly and the noise stops, and the same thing happens in any gear.
I used a mechanics stethoscope on each of the gearboxes and the bellhousing, and the noise is by far the loudest from the bellhousing and gets more muffled as I work back to the transfre case.
Any guesses what could possibly make this noise? The gearboxes are all rebuilt and the clutch is new, so I'm out of ideas at this point but it sounds exactly like the noise in the video from this thread.
video