Let's summarize.
None of the switches in column 3 work in switch test.
You have continuity from the MPU connector to each switch in the column.
This points to an MPU problem.
But, it is odd that the problem began after you worked on the thing optos.
Were you working on the game with power on?

A logic probe would be my tool of choice for the next steps. If you don't have one, set your DMM to DC volts.

Measure DC power between the MPU pin on J206 for the failed column.
Game on and in attract mode.
Remove all connectors on the MPU bottom except the one with all orange wires.
Black lead on the backbox ground braid.
Red lead on pins of J206. Compare the voltage on the "failed" pin to the pins on each side of the failed pin. If close, the problem probably lies elsewhere. If there is a big difference, you have a board issue.

Let us know what you find.

Nice work so far. You can rule out fuses. No need to test them.
--
Chris Hibler - CARGPB #31
http://www.Team-EM.com
http://webpages.charter.net/chibler/Pinball/index.htm
http://www.PinWiki.com - The new place for pinball repair info