Not sure about the exhaust but if you got water inside the car, specifically under the driver's seat, it has likely damaged/destroyed the alarm/immobilizer, which is very expensive to repair/replace. I'm sorry to hear you 986 may be totaled.
If it ends up being repairable, here's a link to an ECU repair shop I have heard good things about
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Specialized ECU Repair, Replacement, & Testing - Restore or Exchange your Electronic Control Unit (ECU)