JCL here says if all your custom chips are OK then most likely one of the small green fuses (that are supposed to look like resistors) might have fried.
It is also possible one of the internal traces has fried.
In any of these two cases, it should be easy to repair the system.
You should check the voltages that comes out of the Zorro III slots. If one of them is dead, it might just be a question of adding a bypass wire.