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Look for a shop that has a good BBB rating, and that has an owner on site, and that actually recommends rebuilds over swaps.
As far as cost, a good shop will do what is called an RDI (Remove, Disassemble, and Inspect), since an accurate quote can never be given when hard part damage is present without partially disassembling the unit.
A shop that is a member of ATRA is a good choice, since most ATRA shops have good reputations, and ATRA has a nationwide warranty larger than any chain.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.