UPDATE:
I did find that my rectifier was busted causing a rattle. I've got a new one on the way. I've already burnt through one set of bobbins on that. This time it was the actual rectifier plate that broke out around the bolt hole.

I did find that the left side exhaust was loose in front of the muffler and tightened that.

I used a tool up to my ear and found that it is loudest when around the bell housing of the trans.

I took the interior out and checked the drive shaft and the bevel box just to be sure. No problems. E-brake line wasn't getting hit. Trans mounts appear to be OK.

It is definitely a strange noise. It is repetitive, but not rotational. Knock, Knock, Knock.....pause, repeat. With some help we were able to determine it happens at low RPMs with the clutch in or out, so that actually tells me if it is mechanical it should be in front of the clutch.

Still waiting to hear back from the mechanic. Maybe MMC has heard something like this before..