My guess is it's a day set aside for taking inventory and re-stocking the shelves.  Perhaps they do this every Tuesday, or something like that.  It may be done while the store is open to customers, or the staff may come in early or stay late, or they may close the store to customers for half a day. 

Now that most stores use a bar code system and scan everything as it leaves the store, the task of keeping track of inventory (stock) is greatly simplified.

The numbers would be the figures (tallies, sales, etc). resulting from the inventory. "Run the numbers" would usually mean to feed the numbers into some computer program which would spit out some kind of summary.   But in this case it means to deliver the numbers to his father, who is in the hospital and is anxiously waiting to see them (I assume).  It's like, "Please run this report over to the main office."  (deliver it   -   carry it    -   drive it   -   as "runners" used to deliver messages.)

  - A.