As mentioned, the COE has a procedure for making changes in public or private involvement thru the Real Estate Instruments chapter of the SMP. In short;
"Real estate instruments refer to leases, licenses or other legal grants issued for commercial or individual activities, which are not covered under Shoreline Use Permits. These activities involve construction of structures, including, but not limited to, masonry walkways, boat launch ramps and parking areas, roads, water lines and power lines. A written request must be submitted to the Project Office, who will make a recommendation to the district office. Each request for a license will be considered on a case-by-case basis. Assistance in preparing applications for real estate instruments is available at the Project Office."
It appears if one had a well-thought out plan and presented it in person to the Project Office, they are obligated to help you get it done.