How do I have a gravel kit certified as an STC?
The FAA has a nice checklist here.

You should read through the FAA's GUIDE FOR OBTAINING A SUPPLEMENTAL TYPE CERTIFICATE. I assume you are a civilian but, 


  This advisory circular (AC) is a certification guide for obtaining a
  supplemental type certificate (STC). It is intended for civilian
  applicants only. We have written it to help designers, manufacturers
  and installers applying for STCs to better understand the STC process.
  The guidance in this AC is general in nature and intended to help an
  applicant gain a basic understanding of the STC process and our
  respective roles and responsibilities.


You will need to fill out this application form and submit it to the FAA ACO office in your area.