When i did mine i did not fiil all of the holes. I left some of the larger one's to run lines and wires through. However after the car is completly mocked up, wired and plumbed i may fill what holes were not used. I also left holes in bottum of frame rail so it could drain. Before boxing i applied several coats of cold galvanizing paint then topped it with primer. I figured that would help protect it. Not extremely worried about water since car will not be driven in the rain and with the water hardness I have, not washed with water very often.
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