Yes, the grinding is exactly what I was talking about while you're in 1st and 2nd..
Again see the following (from above):
TSB - 04-13-4 Transmission Rattle Noise or Difficult to Shift - Tremec T56 6 Speed Manual
Issue:
Some 2003-2004 Mustang Cobra vechicles equipped with a Tremec T56 6 speed manual transmission, may exhibit a rattle noise or a difficult to shift condition. This may be due to a cracked or broken release bearing guide tube.
Action:
To service, install a revised transmission adapter cover plate, The revised adapter cover has the release bearing guide tube already installed. Part-number 3r3z-7005-aa.
The part is on national back order.
Print this out and take it to your dealer. They will order the parts and install-
Good luck.