Okay, since it's a stick, you don't have to worry about the TCU. Maybe a long shot but check the connections to the ignition coils - if one is loose, or the wires are worn/chewed, it might start fine, but after a little while, lose contact, and then that cylinder shuts down (although that would eventually throw a P0600 code, but only after a certain number of misfires). Not all error codes throw a check engine light.
Good Luck