I just had the same thing happen to me, I just had a used SVT engine put in. Cost was $1000 for the engine, about $700 for new clutch and flywheel, and $500 for misc. parts (with careful NON-FORD DEALER shopping, you can pay about half that).
The Spickle
New Car: Infra Red '04 FSVT
Former Car: Black '98 CSVT, #3137/6535 "The Unluckiest car.. ever"