As said, there is a hole to put a long bolt in to hold rod up while installing pump, then replace with short bolt. They never needed any sealer in my experience, wouldn't hurt probably. A copper washer will work if you don't like sealer in there. Post picture of other leaker? Are you sure both leak or just one and spilling onto other? I think you will find the bottom hole is blind. You will find that when you put in a short 3/8 bolt in the top hole, the leak will go away as stated by Don and Jerry.
"These same holes in my other truck aren't plugged and never leaked"... ????????what engine? What year? is it FI? Better double check that!!
