Cabin leaks in rain.

I would start looking at the door seals. Also if water is entering thorough the center top brake light, there is a good chance it can trickle down the inside of the trim and to the floorboards. You can use masking tape to cover the gap between door and body, then run a garden hose to see what leaks.

I had this same issue with a GMC Canyon. After countless hours of looking for a entry point,removing interior,sealing brake light. I got a small mirror and looked at the back of the cab. I found the seam sealer was not installed properly from manufacturer. Took to dealer and they removed bed and finally agreed with me but......it took multiple trips explaining what I seen.