How can someone get clarification from the FAA on the intent of a regulation?
Generally there are two ways to get an interpretation of regulations from the FAA.

The first (less-formal) way would be to call or email your local FSDO with your question -- they will usually get back to you pretty quickly with a verbal opinion or an email (on the two occasions I've contacted the local FSDO I've gotten an answer within 1-2 days).  

Interpretations from your local FSDO are essentially valid within their coverage area (if you get an opinion from Farmingdale in New York the folks in Los Angeles, California may not honor it).



The second (very formal) way is to write an actual on-paper letter to the FAA's office of the chief counsel requesting a legal interpretation of some specific regulation(s) and mail it to their office:  

Office of the Chief Counsel
800 Independence Avenue SW
Washington, DC 20591 


This request should be as specific as you can make it, for example:


  May the FAA hold a person who performs maintenance on an aircraft responsible for the proper performance of that maintenance under 43.13(a) and (b) when that person was not the person who made the maintenance record entry required by 43.9?


If your request is inspired by some ongoing action (say a warning letter) you should reference it and include a copy to help speed things along.

The FAA's legal staff will chew on the request for a while, and eventually produce a legal interpretation (the linked interpretation, which answers the example question above, took about 5 months, and it is a relatively simple interpretation - The more complex the regulation that needs to be interpreted the longer it will probably take).

Counsel interpretations are organization-wide precedent, and on occasion they can overrule opinions/decisions from a FSDO. They are effective "The Final Word" on how regulations are to be applied (unless overturned in court).