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When my 06 GT was brand new - less than 500 miles on it - I had a similar problem. It was nearly impossible to get the shifter to go into gear. I took it in to the dealer and it took them a really long time to diagnose the problem and several failed guesses - replaced clutch, master cylinder, other stuff - I can't even remember. Anyway finally it turned out to be the flywheel. After replacing the flywheel under warranty the problem was resolved.