Can I reach the flywheel bolts without taking out the pressure plate and clutch? I suspect the previous owner may have missed something in his assembly of the clutch and transmission as he worked periodically on the truck over many years. Seems like a good way of losing track of what you did and forgetting something. I took off the dust cover and found no shaving or anything suspicious there. I looked up in the bell housing and did not see anything obvious. Could a loose bolt make this kind of noise or would it have to be backed out and hitting something?

I guess my next steps are:
1. Pull one wire at a time while running and see what I get ( I forgot about this one till now that I reread everything again)
2. Remove the trans floor pan and listen to see if I can get a better idea if its flywheel related. There looks like a little door on top of the bell housing, maybe that will help see something. With the bottom dust cover on, If I take the small top door off the bell housing and the sound increases then that's the problem area.
3. Drop oil pan and see what there is to see.
4. Remove timing gear cover and see if the fiber gears are good.