What I have learned is you can never keep water out of a tool box. In the "jobox" I installed in my B2, I drilled a 1/8" hole in each corner, and one along each edge, so it can self-drain. Since mice can supposedly squish through a 1/4" hole, I do not go up to 1/4". Though I drill 1/4" inch holes into the corners of my small hand held mobile tool boxes, since they are the ones most likely to receive a bunch of rain, and are more likely to collect gunk that could plug smaller holes. Inside my bigger boxes where I store food, I put them inside cookie tin cans and sometimes seal the edge with foil or masking tape for bugs.
On your box, I guess you are planning on a hinge and not lifting it off? I would drill 1/4"-3/8" holes in the lip area between the inner and outer wall, along the whole perimeter to drain water and muck.. Make a cover that recesses in between the gap. Put a tab on the cover and a tab at the back of the box inside the channel. Use the only combo lock worth having on it for security, Abus 190/60CS series 2.
I use eyelets on many of my boxes to help secure stuff with straps or bungees inside my boxes, though a welded on tab would be better. Putting a cut up rubber floor mat under floor jacks helps protect the finish.
If you take vacuum line, cut a slit down the middle and put it over the edge, when pressed down by the top it should create a good enough seal and prevent rattles.