I don't have factory alarm but I did just program another fob to the keyless entry system and it was pretty smooth. I followed the procedure you are talking about (exact steps were found on this forum, but you'd have to search).

As for the locks getting weaker towards the 5th cycle, that'd give me the impression that the lock actuators are starting to give out. Kind of a coincidence that they'd all go, but not unlikely either given the age. I'd study up the procedure and feel confident doing it so that when you execute the procedure you don't keep messing up and having to redo it- that'd definitely wear your lock actuators. If it does get to that point, let them "rest" for a lil bit to allow then to cool down and prevent further wear. Hope this works.