A bad battery can cause the alarm to need a re-set or more. It may be that your alarm failed. This can be a tough situation, because a factory alarm is really hard to bypass and, it is next to impossible, I find in my every day shop experience, to find Ford parts that are more than about 12 years old from the factory. They stop making them after about 10 years, which I think is horrible. I often have to have cars donated for Smog Repairs in Calif, just because there are not factory parts and the after market does not make them, say like EVAP parts. I would try a good alarm shop and see what they can come up with, maybe they know how to get around the factory stuff.