Lets try this. Unplug shore power and with the breakers on the generator tripped (just to in case it somehow starts) go the transfer switch and the breaker panel ensuring ALL the wire camps are tight.
If everything is tight but still missing half the bus head on down to you local big box store and pick up one of
THESE. If you have a meter already then just get non-contact voltage tester. Makes chasing lost AC power very easy.
When you start digging into the transfer switch there might be a wiring diagram on the cover which will help.