Take it apart soon and you won't have rust where the rotor seals are in contact with the cases.
I bought a miata that was a Harvey victim. I bought it two months after the flood and refurbed it. It currently has had two track days and is on its way to being a spec miata. The flooding was from fresh water due to an overflowing bayou, no saltwater.
There is likely water in every fluid - engine, trans, and diff.
Engine should be gone through like it's being overhauled. The flood water enters through the seals and through the open valves (or ports in your case). There is silt and dirt in the water. Engine must be completely cleaned including the oil galleys, heads disassembled and valves cleaned (exhaust valves had a bit of rust). However, the oil floats up and tends to protect the bores. There were rust spots were the rings were sitting on the cylinders that luckily ball honed out. Otherwise, the bores were clean. If you disassemble soon you may avoid this. Sealed bearings aren't that sealed. The timing belt tensioner idler bearing was frozen.
Same with trans and diff. You may be able to get away with partial disassembly and inspection. I did on a 5 speed standard and my rear end didn't have any water. The clutch was a mess. I could have cleaned up the pressure plate if I wanted to.
Gas tank had water but no rust. Water/corrosion caused the fuel pump to seize.
All the electrics necessary for a race car worked fine. The alternator got silt in the bearings and needs to be replaced after second track day. The ECU and dash console work fine. headlights, taillights, signals all work. I don't know about the rest (radio, window motors, etc.) because they were tossed. Almost all of the plugs and connections need to be unplugged to pull the engine or the dash for a rollbar. I unplugged the few remaining plugs and connections anyhow for assurance that they were clean. I assume mid 2000s RX-8s and miatas are similar.
Rebuild or replace the wheel bearings. Mine seemed fine but I replaced them.
I could have refurbed it for the price of a gasket set if I was trying to stay with in the "$500" Lemons limit because the rings and bearing were ok.
In the end, it was mostly man-hours and a lot of it you would probably do for a thorough build and prep. Everything functions well.
Go to Copart.com. There will be a lot of flood totaled cars for sale.
