I pulled my over rail liner today and found two factory punched oval holes in the bed floor just to the left of center at 1/3rd intervals from front to rear. There were two larger ones on the lower bulkhead wall behind the cab.
What are they for? Especially curious about the two on the floor

 

Floor I believe is for drainage but not too sure. The front is probably for access of extra wires for accessories. I used a front one to run wires to a pump that I use on my 75 gallon extra fuel tank.

 

Holes drilled in Bed floor are to let the water drain out.