I wouldn't do anything to the trans and when I did my Forged Rebuild at 59K the stock clutch actually looked perfect so I reused it and it's still feeling great! Just take a look at the disc for wear, you could throw a Fidanza Aluminum Flywheel on while you have it apart though!! 
Also if you considered adding the Cooling Mod it's easier to do with the motor pulled!
__________________ 99 SVT Cobra-Stock Teksid Block .020 over,Balanced Rotating Assembly,Manley Forged Pistons & H Beam Rods,Forged Cobra Crank,Stock HCI,Total Seal Plasma Moly Rings,Federal Mogul Bearings,ARP Studs,Melling Billet Oil Pump,Mac O/R H & Durablack 2.5 Catback,JLT RAI,Vogtland 1.6 Springs,Maximum Motorsports CC Plates,Subframes,Steeda Tri-Ax,Nitto 555's,U7146 Predator,Custom Diablo Tune,Member 7 Quart Club! 314HP/307Torq
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