The only real problem I have heard about is the 2nd gear syncros in the T45 being prone to going out, which I think I may be starting to experience on my 28K mile '00 GT. Shift that sucker fast and at high revs when you test drive it and make sure it engages each gear smoothly, especially 2nd.
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Strike down the unroadworthy!
2000 GT Atl. Blue: '03 Cobra motor - 465rwhp/473rwtq, T-56 6-speed, full MM TA/PH & tubular K-member suspension, Saleen body, 17" Torq-Thrust II's, M/T ET Street radials, and lots more
'94 Rio Red Cobra: All the bolt-ons, 3.73s
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