do you think the new rum needs a roof or could it just be chicken wire? I’m also considering construction sand for the run which will be elevated above the ground level to prevent flooding.
So roofing is up to you... is snow an issue where you live at all (probably not, but I won't assume)? If not, then a wire mesh or bird netting should be no issue for a run topper.
Is rain an issue? Since you mentioned flooding, if the area floods is it due to direct rains or is it an issue with the location being low lying? If the spot floods due to rainfall then a roof would help a bit, if it's moisture that wicks/flows in from surrounding area, then the roof won't make a difference.