Autopilots destroyed by spikes?

I have had 3 Raymarine Type 300 autopilots electronics destroyed in 3 years. With the help of Raymarine I have determined thatit is possible that the electronics are being destroyed by spikes or surges on the 12 volt supply. These spikes/surges may be caused by the bow thruster and windlass being wired to the same battery bank (400ah) as the autopilot, or there may be some other cause - fridge bilge pump etc.
How can I protect the next new (and expensive) autopilot computer from destruction? The autopilot is fused at 40 amps