Has anyone any other suggestions to make regarding protection for this exposed and expensive item?
Return the replacement which I assume is the Cycle-Electric rectifier that S&S supplied.
Get the HD unit to replace it as it will be only a third of what you paid. Remove the rubber bobbins used to protect the C-E unit as they won't be needed. Bolt directly to the mounting point either in front like the older models or on the side.
Drive.
No bikers I have talked with have any respect for the C-E unit. It is supposed to constantly vary the current depending on load. They call it 'delicate' or a POS. The H-D unit just converts everything and dumps the excess to ground like all other bike rectifiers. Do one thing. Do it right.