I tried to skim the thread, sorry if any or all of this has already been suggested. The magic cocktail for me (so far, knock on wood) includes:
1) Router and dust collector power cords routed off the opposite side from the C3D board into a different circuit
2) Anti-static dust collector hoses
3) Connection from computer to Shapeoko as follows:
Powered USB Hub ->
Industrial USB Isolator from Amazon ->
Very short USB cable ->
4) Sacrifice a rubber chicken to Kek.
(Just kidding about that last one).
Ignore this if I'm just repeating things already suggested.