If the elevation works out, place a piece of 6 or 8" pvc around the cleanout and pour a small pad. You can use a coupling and add a cap to keep the dirt out and protect the opening. Recess the cap enough to get the square on top below surface height. Another option is to leave a square opening with a shoulder to accept a plastic grate which you can get at any home supply store. This should leave access to the cleanout and eliminate your rot problem.