pbilt:
Your description is kind of difficult to diagnose. I'm not familiar with the M5R1 b/c my 87 has the Mitsu FM145. But when I had a rumbling type noise, I followed the excellent diagnosis section in a book by Robert Bowen called "How to Rebuild and Modify Your Manual Transmission". Starts on p. 46. It takes careful reading, but it helped me.
Turns out I had a broken 5th gear set. So I rebuilt the tranny (my first manual tranny rebuild). I recently bought a couple of M5R1s dirt cheap, but when I pulled them apart I found the mainshaft shift-gears were shot (the trannies were abused and slammed into gear so hard that the shifter teeth on the sliders, gears and synchros were flattened out).
In addition to reading the book (check your library or spend $25), have a guy who owns a truck with the M5R1 test drive you rig. Or drive his. Compare the noises. That would help a LOT.
And I recommend keeping snide comments to a minimum. Rednine was only trying to help.
If you decide to pull the tranny, folks here can tell you what to look for as obvious problems. You can't diagnose a bad bearing by spinning the shafts by hand (unless they are so bad that the noise would be very noticeable). The only thing you can tell is if the input and mainshaft bearings are trouble because the shafts (input in particular) will move quite a bit. My tranny's input shaft moved a little bit and it was noticeable, but it's rock solid after the rebuild. I'm pretty sure my bearings were serviceable -- that 5th gear was NOISY when a tooth broke off. That got my attention!!
Good luck. Let us know what you do and what you find out.
John