If the holes in the floor are letting water from the leaks in the window seals drain out the bottom. Leave the holes in the floor.
If the windows are leaking, you are pretty much screwed, so enjoy life and ignore the holes in the floor, but acknowledge this and don't ruin the carpets by reinstalling them.
If the holes in the floor are NOT related to leaking windows, wait until the windows leak, the sills rot out, and THEN fix everything at once. This will also provide adequate time to let the rockers rot out, so everything will get done at once!
Whatever you do- do not jeapordize the carpets.
Hope this helps.
Ron