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you have proved that the smart charging is working.
i would say that you have a fault with the instrument pack.
i would advise that you stop here before you spend more money you dont need to.
get it to a ford dealer or a reputable independent diagnostician, and have it plugged in with a scanner or IDS/ WDS.
you need to get some fault codes out to get a more precise idea of what is going wrong here.
the smart charging system is not all built into the alternator, - it works as part of a program strategy built into the engine management system, and i cant be sure - but possibly the instrument pack.
however with all your random light illuminations i would suspect that the fault is with the instrument pack.