Dan - Other than having the holes welded closed l would buy a 12 x 12 inch piece of 18 gauge sheet metal from a big box store or ACE, cut to size, pre-drill for pop rivits. I would also use seam sealer between the metals and coat the entire underside. Water pumps don’t use a conventional lip seal, they have a carbon type seal so they will wear out but not age quickly. What looks like a pipe plug is actually the kickdown band adusting screw, look at page 216 in the service manual. The large lockdown nut may just need tightening dont move the adusting screw.. It won’t hurt the tranny to sit with no oil but l would not leave it without the pan on it.
Have fun,
Dick