after hard rain, radio and door locks will not work

Not knowing the extent of flooding of your JXi, I can say there is an amp under the passenger seat that was probably submerged, along with other wiring, that has shorted out. Fully drying the interior first, (possibly requiring carpet+pad removal) then checking all fuses (under hood and in dash). The owners manual would be a big assist to track the blown fuses. I imagine the amp is shot if it was soaked. The weep holes should be cleared with a toothpick and checked seasonally,especially in dusty or high pollen areas. Careful cleaning & drying of wet areas is imperative to prevent mold formation and corrosion. Borax powder dissolved in water scrubbed into carpet and pad then dried and vacuumed will eliminate mold and mildew.

Tops are a big issue on these cars if the back glass has popped from the top it will need replaced to stop further water damage the amp if wet when energized is toast salvage yard item or ebay tops are avail starting at 358.00 i do not recomend the plastic window as it will "fog" in about 6- 10 months forcing you to replace it again. The heated glass is what i just put in mine the top comes installation instructions and was fairly easy some special tools (starbits) to get fabric off and replace it. Too see if you need a top which it sounds as you do, the top should be completly sealed no curls open voids,or visible holes use the tip of your finger gently inspect the bottom of glass at this point the leak will be obvious.

On the deck indicator theres a small black wire by itself clean connection w wd40 and actvate it several times high humidity climates make the trunk "sweat" causing corrosion

check the radio memory fuse. mine was blown causing the trunk lamp to stay on