As you said in your question the Rule says "In side view no portion of the brake system that is mounted on the sprung part of the car can project below the the lower surface of the frame or the monocoque." From what you describe, your system did not meet the Rule. I think the wording is perfectly clear. We do try to make the wording of all the rules crystal clear. If we were to add "the intent" of every rule to the Rule Book, we would end up with a real tome! If you can suggest a better wording, please let us know.
The confusion came from the interpretation of the definition of "lower surface". The implication of what the inspector told us was that "lower surface" meant the lowest point. This was because there was a frame member that was beneath the brake assembly, only it was rearwards, not in front of it. The inspector said if the lower frame member had been forward of the brake system it would have been ok. This implies that "lower surface" means the lowest point, not that there necessarily has to be a frame member directly below the brake system. The intention, as was indicated by the inspector, was not necessarily that a frame member needed to be between the components and the road surface, but that there was protection from a curb impact. I am not sure as to how you would reword the rule. Here is a quick drawing of how our frame was designed and where the brake system was located:
I understand that the rules committee puts a ton of effort into making the rules clearly reflect the intentions of the rule, I am just bringing up these questions in order to help other teams that may run into similar questions, and to clarify for our future vehicles. Thank you for you time addressing this issue!