So I went through this issue with my Mustang. You can do it yourself, but you may need a dealer for the PATS (passive anti-theft system) part if yours is completely fried. The PCM for a Raptor isn't that expensive I don't think. You'll need a J2534 pass through device for the programming. You can buy one from Amazon for around $500. I recommend the Mongoose Plus. Then you'll need a 2 day subscription for FJDS or FDRS, which you can get on the motorcraft website. If you somehow have access to a VCM II, you can use the real IDS dealer software, but it's not necessary.
After all that, the programming is super simple. There's lot of videos and training available online. If your PCM is truly fried and the software cannot talk to it, you'll need to grab as-built files from Ford, which I can point you in the right direction. But you'll probably have issues programming the PATS part.