Check ebay for a motherboard, it showed one system board (from Poland though) and a few ship laptop to us repair prices which are a lot less than $400. I can't vouch for any of those services so check the ebay ratings for them.
Depends on how the jack failed, you may be able to solder the jack to the system, check with a different repair shop. Also check with MSI because it should not be breaking like this, they may extend the warranty. Things like this will be tough to prove that it was not done by mishandling just because you say it was not. Check online for other people that may have posted about issues with that model.