Noticed 4 inches of water in my rear passenger footwell this morning. After getting it all out, the floor felt like a water bed. Had to peel back the flooring to find rust soup. Another 2 inches of rusty ass water.
Do you happen to have a sunroof? There are drains running off sunroofs down the A and C pillars that can get clogged or burst due to age.
Check the underside of both front and rear doors on that side of the car for a small drain hole and stick some clothes hangar wire up thru them. Contrary to popular belief, the window seal where it slides down into the door is actually incapable of sealing- all the water simply runs down the outside of the glass collects in the bottom of the door, and is drained out the bottom on the outside of the rubber weatherstripping. When these drains get clogged the water backs up and flows inside the car.
I'd recommend checking the roof/etc for any custom mounting holes that may have been incorrectly sealed or have been compromised. It's possible that when it was decomissioned there were holes that got plugged (lightbar, antennas, etc) and have not held up. I'd also check the weatherstripping on top the door frame to make sure it's sealing okay.