I was actually working on the Shadow yesterday and had the same problem. For me it was because I forgot to plug in the drop bank connector (doh!). You said you tested the coil in solenoid test and that you tested if the drops knocked down individually but you didn't explicitly say you tested them in switch edge test mode. Did you run that test? The switches should be normally closed and open when you drop them. If that doesn't work that strongly suggest something is wrong with your optos / the board with the optos.
I don't think you need a logic probe the test them. Just put your multimeter in resistance mode (audio beep mode) probe the row and column of each switch with it closed (drop up, should beep) and open (drop down, should not beep). Unfortunately since these are optos this test is only going to work with the power on. so take the necessary precautions.
(PS, you have 14 pins already!? When are you going to host a DFW pinball league? You should come to Ken's event this afternoon. Lots of experienced pinheads can give you advice on your problem).