There are two (2) TSB's (Tech Service Bulletin) that seem to be directly related to your concerns:

TBS: 9-Mar-04 - 21-002-04 - Manual Trans - First Gear Disengages During Normal Acceleration
TBS: 6-Jan-05 - 21-001-05 - Manual Trans - Gear Grind Sound When Shifting

Not sure how it works with TSB's, but I think Chrysler should honor regardless of Warranty.

I'm sure someone will chime in and clarify...