This car is an amazing car and for a JXI for $1600 with only 90K miles was too good to pass. Has a few issues with it now but nothing major at all. Here's the backstory.
The first week I had the car we had very severe rain for a couple of days and me not knowing the drains needed to be uncloged. Needless to say my car flooded. I started the car and the speakers were making a loud sound so I turned it off. The noise continued and after a couple minutes just stopped. The amp under the passenger seat was submerged during the rain and the radio stopped turning on after this incident. Also the lighting when you open the doors stopped working. It now reads "deck" every time the car is turned on even though the trunk is closed.
Is the radio or amp any good?
Do I need the whole bottom rewired?
Also my dash lights only work occasionally but I have seen other threads saying the inverter needs to be replaced.
My fog lights do not come on at all since I bought the car.
And the keyless entry only works with the car on. Defeats the purpose of keyless entry.
Any advice would be great, thanks

 

The chances of the amp surviving being submerged are not very great. It's pretty tough to find anybody willing to repair something like that these days. "Throw it out and replace it" is usually more economical than trying to repair it.

Rainwater probably won't ruin the wiring assuming you have dried it thoroughly and quickly. Letting it sit wet is an invitation to corrosion at the terminals.

For your dash lights, go here:

Speedometer Repair | Instrument Cluster Repair | Odometer Repair | Mr. Whizard

They respond to questions there.

Check the fog owners manual for the fog lamps. They usually require that the headlights be on but not on high beams.

Check the IOD fuse. Otherwise, not sure what's going on with the keyless entry.