05GTPONY

Can anyone recommend buying a "Take-off" 6R3Z7003AA 5 speed Manual transmission for my 05 GT? It's in the shop and Ford wants over $2K just to replace the bearings, etc. Also I'm told my input shaft has 10 splines on it and my output shaft has 28. The two take-off tranny's i found one has a 10 spline and the other a 31 spline. Confused about which one i need?
Also they said I need a new clutch. Would it make sense to buy a SPEC or other performance clutch? I don't want too heavy duty a clutch since I do drive it everyday. Can anyone recommend a good one? Thanks!