The PCM, starter, alternator, and wiring were all submerged except for the dome light. It is difficult to determine what/where the problem area(s) may be, but until it is dried out completely any efforts to diagnose it could be difficult.
Keep in mind that a failed alternator will not prevent cranking, and a battery that has been submerged is ready to be recycled. Everything else is a wildcard. The injectors and fuel pump are probably intact, but the fuel tank likely has lots of water in it. The ICM is likely intact but soaked. Most sensors are probably intact and could operate once dried out, with the possible exceptions of the TPS, and the IAC is likely waterlogged.
At the very least, it would be advisable to remove all the spark plugs and manually turn the engine over at least two full revolutions (more would be better) to expel any water and prevent hydrolocking and piston/head damage.