Hi,
you are talking of high powerful voltage spikes.
What comes into my mind:
* Dou you have a proper power plane, so every voltage can rely on that voltage?
* Use one path for signals and other paths for power, so that the power current has no influence on the signal voltages.
* use filtering in the power paths and in the signal paths, maybe inductive or capacitive or both.
* use TVS to keep induced voltage low.
A picture or a schematic could help us to better assist you.
Hope this helps
Klaus