To handle the solder bump just back drill the upper layer of board to provide a place to put the solder joint. Only needs to be done on a few holes in this case, and then they will be flat.
Very nice Fran, you are making a replacement for an old IBM mini look there, just need to get a stack of the aluminium cans that were used on the IBM logic, and a board with lots of via's on top and bottom in a pattern, then you can build IBM style.