Here's the post stamp cited with wiring diagrams/pcm communication .... if its the right year?
http://www.expeditionforum.com/threads/charging-system.35838/#post-304461
some good info but this is getting a bit knotted up (methinks)
the key is a disciplined diagnosis (sorry to state the obvious) .....
what exactly did pep boys find was not working right when they decided to replace the alternator? what changed (if anything) with new alternator? if EVERYTHING is exactly the same with new alternator then they probably should put the old one back in and refund $$$??? then chase down the original problem
it is possible to have more than one problem at the same time (sometimes 3), especially with parts swap -- confounding diagnosis. could be a connection was defective causing original problem then new alternator has that pcm/communication issue so now 2 problems. not saying thats the case, just possible
i'm not really knowledgeable about that PCM communication concern but if there was no communication between pcm and alternator then it would seem that would be easy to observe by measuring voltages & signals, is that true?
i would not replace fusible link without diagnosing an obvious problem with it, what is the observed problem that shows fusible link is bad? the charging light coming on cant prove fusible link is bad, other evidence needed to indicate that
a skilled mechanic can use tools like in this video, along with knowledge of the system to find out whats wrong
i'm not a big fan of swapping parts (like alternator, battery, fusible link) without hard evidence that they are bad (how/why)... and then if you do, hard evidence of a problem corrected by the replacement part
hope some of this helps