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Hello. My name is ***** ***** I am happy to assist you today. Give me just a moment to review your post, and I'll be right back with the help you need.
When you scan the computer system what are the fault code and or codes your getting?
Can you recke them when you can and post back with them and we can work from there. All fault codes should be 4 digits.
This code sets if the charging system is over charging, what is the charging voltage at the battery with the engine running reading?
And you sure the code is P0563?
Once you get it reconnected and running again can you recheck the fault codes and see if this is the code your getting?
Okay let me know.
The charging system is controlled by the duty cycle from the PCM and its not likely a alternator issue you have going on here but maybe a PCM issue. Let see what the fault code and or codes are that reset.
The PCM (power train control module) is the computer that controls the engine management system. See it in the link below.https://dl.dropboxusercontent.com/u/104923897/PCM%20Oct%2019.pdf
Its not hard to replace but will need programming but I would not replace anymore part just yet. Lets see what the fault code and or codes are that reset the next time it goes into Limp mode first.
Are these new OEM Ford alternators your installing?
Im suspecting you may have a bad PCM if your sure the new alternators are okay but I can not be sure from here. I can open the post back up for you if you would like another opinion.
Your very welcome and thank you as well.