The smart charge system on Fords allows the charging voltage to peak at around 16 volts,that is why it is important to use a calcium battery.Alternator output is controlled by the engine ecu but is very rarely the problem.The system needs to be checked correctly,especially the 3-pin connector that is attached to the alternator.One of the wires is a battery voltage sense line,if this is broken or a poor signal,then the system will not operate correctly.Most of the charging faults on late Fords are usually wiring or alternator problems.hth

The engine ecu is partly in the engine bay and partly in the cabin.It is mounted in the bulkhead/firewall.All the basic tests are done at the alternator with a test light and meter..One of the small pins in the 3 pin plug should br battery voltage.For more conclusive tests will need a scope.hth