Have Ford Questions? Ask a Mechanic for Answers ASAP
Hello and thank you for your question,On your 1999 the PCM has no connection to the charging system and will not affect the alternator ability to charge. Do you have access to a 12 volt test light and or volt meter to do some testing?
In order for the alternator to charge you need battery power at the connectors at the alternator on the black/orange wire and the orange/lite blue wire and the green/red wire with the engine running. These wires need to be checked with the connectors plugged in to the alternator and the engine running, check them for me and tell me the results and I will advise you from there. I have also enclosed the wiring diagram for reference for testing. All three wire need battery voltage while running in order for the alternator to charge. Before you start your testing be sure to check the #11 20 amp fuse located in the under hood fuse panel as well as the #30 30 AMP fuse located in the interior fuse panel.https://dl.dropboxusercontent.com/u/104923897/ALT%20Nov%2017.pdf
Run the steps for me and let me know if you have more questions and or need some help and we can work from there.