95cgl -
Did you verify your "original warranty start" date through Ford's OASIS system? The 10 year date is from that date (usually the date of first retail sale), not date manufactured. However, if your 10-year date is September 25, 2005, the dealer isn't obligated to help you.
That said, a cordial discussion of the situation (have a printout of 99M03 with you) might convince them to help you out. Cordial is the key: They need to view you as a potential long-term customer, not just someone who wants work done today.
Sadly, some dealers fight 99M03-related work. As I understand it, it's difficult for even a skilled technician to correctly complete the harness change in the time allowed by Ford. Apparently, labor charges over the allowance are eaten by the dealer (or the technician!), so they avoid doing it.
I had my '95 harness done late last year. As it turns out, I still had time: The car wasn't originally purchased until late 1996 (it was a leftover; the 96's were already out). I was pleasantly surprised: The dealer didn't push back on the work, and replaced all affected harnesses.
