"My strange almost but not quite a grinding noise is back again."

I had a similar problem a couple of months ago.  I'm not sure if the manual transmission mount is the same as the auto trans (like I have) but here's what I found....
Unbolted the trans mount and found that the rubber isolation damper thinger was pretty rotten, allowing metal to metal and causing wierd vibration and noise while driving at deceleration and acceleration and certain revs.  I used a bunch of hot glue gun glue to pack in around the rubber until I can replace the bushing and it is nice and quiet now.  Worth a check anyway.
Brent

Brent Weide
Portland, Oregon
http://www.weidefamily.net/vanagon/