Call an irrigation tech in your town..he has just the tool you are looking for...well, not all of them have it. You can also call a parts house in town that may rent it to you, but the rental fee may be as much or close to the same cost to have someone find it for you
This tool will trace the wires to the missing zones and locate the box quite quickly.
Good luck!
Sprinkler Solutions, Inc.
Arizona and Colorado
www.sprinklersolutions.net