These are available at your local Toyota dealer. Have finally found the solution and no, I have no idea why there are in the floor other than maybe something for a right hand drive. The "official" drain hole is larger and next to the A pillar. Anyway, these plugs are a perfect fit and now I can sleep at night
On the passenger floor, forward of the fuel tank cover and about 7" left of the side of the body. A lot of FJ 40's have these two holes. Apparently the reason for them is not readily known. In my photo the passenger seat frame is visible in the lower left side of the photo.