Get and print your phone records showing every single call you made to the auto shop.
Get a lot more pictures, especially of the wiring that's left. Get close ups of every connection, every sensor, top, bottom, sides, everywhere they could have remotely, possibly have worked with a connection.
Save everything, every scrap of paper related to the build, and any all work and or parts you bought, including the battery.
Get a copy of the Mopar/Jeep FSM, the real one, not a Chilton's or anything else. (For wiring comparison in Small Claims if you go there).
If you have time or have someone who can do it take the Jeep to another mechanic/shop, ideally a one that specializes in and has reputable certification in auto electrics. Have them try to determine the source, and cause, of the fire. Worth the money...
Your insurance may be at least pay for that part or recommend someone they use. Unfortunately, something changed in the management of USAA and they are developing a very bad reputation...
Document everything you do
Contact the SD Small Claims Court Advisor Office, they can offer good free advice. You can file a claim before you deploy and the Court and delay hearing the case until you return. Small Claims Advisor
Best of luck, keep your head down and let us know when you get back and more importantly, thanks for serving