I had the exact same issue with my 99 SVT. With only 16K miles on it, the dealer (very reluctantly) replaced the flywheel and throw-out bearing. Fixed the problem. I would highly recommend looking into a warped flywheel issue.

1999 Contour SVT #1966/2760, Silver Frost/Midnight Blue Koni Kit, Mille Miglia MM-S rims, B&M shifter, Stazi mesh, SFCs, optimized Y-pipe & TB, SS break lines, K&N drop-in, Infinity Kappa speakers, MTX amp/sub