Sorry this is causing a headache for you.
The SDB is not responding to commands from the MPU board to activate solenoids so the first thing to do is make sure the SDB is receiving those command signals. If these signals all test ok, then the Alltek SDB is suspect.
You mentioned the connectors have been re-pinned - are you sure none of the terminal pins accidentally got squashed too much and aren't physically touching the pin on the board? Below I've posted a picture of a connector and how a terminal is gapped too much and not making contact with the board pin.
Grab your mulitmeter and set it to DC voltage. Hook up the black meter lead to ground somewhere.
Start the game and go to the solenoid test mode.
See the picture of the Alltek SDB below - sorry about the poor quality but it's all I can find that's published. To the left of the J4 header connector, you can see traces running from the J4 pins to a tiny black resistor network with tiny legs on its side.
If you follow the pin/signal marked CB2 and put your red meter lead where that signal goes to that black resistor network, you should read 0 volts while in solenoid test mode.
Do the same with the signals marked PB0, PB1, PB2, PB3. Keep your red meter lead on these pins during the solenoid test - when certain solenoids are supposed to activate, some of these signals should briefly change from 5 volts to 0 volts. With these signals you are basically looking for the quick change to 0 volts happening.
I hope this all makes enough sense for you to follow. If not post a nice clear pic of the same area pictured below so I can detail better where to measure.