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From: In between Your Mom's Titties, skeet skeet..
RE: 1999 Cobra Transmission stuck
I'd venture to guess that the shift fork may be broken or disconnected somehow.. How does the clutch pedal feel?? It is even possible that something is jamming the shifter or binding in the clutch quadrant..
I had it happen to my gt. I jacked up the rear and put it on jack stands, chalked the front wheels and wound it up a couple times while jiggling/trying to get the shifter unstuck. It worked but I never found anything wrong but I seized the opportunity to replace the shifter with a Tri-Ax. That was 2 years ago and I haven't had the problem since.
Try taking it out of gear when the car is not running. If it won't come out even then you have a bent or broken shift fork. Its a common failure in the T-45.