Look... I like a dip in a redneck hot tub every once in a while... You line your pickup truck's bed with a tarp and fill it with water. Bypass the radiator and run the coolant lines through, then let the water pump do its thing. Add exhaust for soothing bubbles.

But the RX-8's trunk is WAY too small for such shenanigans.

It rained and I found my newly purchased trunk a bit damp and there's some rust under the little plastic tray that holds the jack and towing/recovery eyes... Crawling under the car, I see that there's two drain hole rubber plugs and the area around them is a bit rusty.
I'd like to drill out the spot welds and have a new panel welded in. Is there a part number for that panel?

I'll do this AFTER diagnosing the leak. I'm seeing all manner of sources of the water from the tail light seals to the trunk weatherstripping to even the polyurethane sealant around the rear glass.
Still looking, but after I fix that, I'd like to hit the body shop as cancer is no joke.

 

dont recall seeing a trunk floor patch panel. maybe look for a wrecked or blown up 8 being parted out

 

Does the car have a sunroof? If so, perhaps clogged or leaking sunroof drain lines.

 

No sunroof.

 

Just tossing out a couple of ideas here. If the trunk seal is visually good and is still pliable, I would look at the rear spoiler mounting points. I have seen some leak where the spoiler bolts to the body. This is a result is either a faulty seal around the studs where the studs protrude through the trunk skin or that the mounting points on the trunk have some rust and the rust is allowing water seepage into the trunk.

If I remember correctly, the S1 (I know you have an S2) has spoiler mounting points that are pretty far outward on the trunk. This should cause any erroneous water entry to gather in the channel around the trunk. But just thinking perhaps the water is running down the channel and weeping past the trunk seal in the center at the lowest point and getting into the tool kit case, causing some rust. Just something to think about. From the picture you posted of your car, it appears to me to have a small rear spoiler and that's why I mentioned this.