You should be able to get the missing letters to show up looking at the matrix and jumping the correct pins on the keyboard socket with a little jumper wire. So quickly jumping 2 and 16 should make the O show up.
The only other thing I could think to test would be to see if pins 1 and 2 on the keyboard connector are shorted to ground or together.
The 2 switches are each separate circuits
The keyboard missing letters are separate circuits.
What do all of these non-connected things have in common? The PIA. PIA's do go bad.
Maybe the PO plugged something funky in to the joystick ports that fried the PIA.