Sorry, just saw this today. I'll take a look when I get home. It's probably around 1/8", it's pretty thin.
A nylon screw would be ok to fill the holes. The problem w/ the holes is the threads give out too easily. And I don't see a need to get fancy w/ the building materials. I'd use a hot glue gun and tape some wax paper to the inside to keep the glue from spilling into the box before it cools. Remove the tape and wax paper when done.
As for making it a low water level area, the trick is securing it in place. As the water level in the box goes down, the buoyancy increases, increasing the upward pressure on whatever you use to hold it down. Also, the water crashing into the box tends to make the center of buoyancy / gravity (which ever) change so you will need to either have a very secure spot or secure it in 2 locations. fwiw: After the threads wore out, I used to use a wooden shim between the pump and the box to hold it in place. It worked about 90% of the time.