I wanted to pass along that I laid 12x12 inch ceramic tile directly over the vinyl backing in our kitchen 3 years ago. No problems have surfaced to date. No grout cracks, tile cracks, etc. I did use a latex modified mortar (TEC 345). I also made sure the floor was very solid prior to the installation.
I like your method of leveling. The piece of plywood will give a good level reference.