If the megafuse or fuse 5 is completely blown, the charge light will be on continuously. If it is "partially broken" or some wire connection is loose, then you could get a flickering Battery/Charge light. An alternator with bad brushes or regulator could also give a flickering light.
I would suggest going with a FORD OEM BRAND NEW alternator. I think it is about $170 but it will be worth every penny. Some have had to replace rebuilt aftermarket alternators many times and it is not a fun thing to do. Yes, it is warranteed for lift but you have to pay for labor to reinstall again. I have to say that the Zetec 2.0L alternator is way easier to change than a Duratec 2.5L.
