Update: So in the end everything kind of worked out my insurance stepped in and took care of the water damage bill i ended up only paying the deductable. They tried to tell me its the roof cassette, then they said my valvetronic is bad, in the end that was all bull$hit in the end i saw that they were after the cash, but when my insurance stepped in and sent the adjuster out to see the issues they were reporting all problems magically went away.

Btw iv had tha car back 2 weeks now and its in great shape no check engine lights and the water intrusion has been fixed. it was wires in the rear passenger side harness, they did a shitty job fixing them but at least the problem is solved.