Ah man..... I'm so sorry to read this. Although I must say I'm glad you are ok to be typing. I feel for you, I had $39,000 in damage done to my jeep when it was 10 months old. While mine was not water damaged it was still disheartening. I love the WK2's all the same as as the WK1's.
I can't see the pics on my phone so I can't see the damage done, but here are my thoughts......
Let the insurance fix it to your standards, this is what I did and I was EXTREMELY selective as to the shop I used which took four months and was well worth the wait as they used only Mopar parts and did an impeccable job. Then I began my build for power and speed, which is what I would do in your shoes now that there is tuning available. Make it fun, make it yours and have a blast!
It won't be cheap, but you would be a pioneer in your platform! Did the engine survive?
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Troy built 2010 Jeep SRT8, Dings Racing forged 392 stroker, boost reference return style fuel system, Mondello heads & manifold, ARH 1 7/8" LT's, Off road midpipe, stock cat back exhaust, ATI 17% OD pulley, Stage 6 2-step, Fluidyne radiator, PP built Nag1, remote transmission cooler, PP Dom. TC., 6,500 PTCM, Wavetrac rear LSD.