It's always that damn third gear. Welcome to the club. When mine went I stripped every tooth off third and it's counter. The resulting carnage chewed up all my synchros and while the shaft was still spinning the busted off teeth got caught up in my other gears too. Then came the TKO 600. Freakin awesome trans. You'll love it.
My brother took out his stock T5 (100K miles and an easy 50-60 low 12 second passes) $450 later and it was rebuilt and back in. 35 miles after that towed it to the track, and ran low 12s powershifting every gear. I love abusing these things (until I pop mine that is).