It sounds like your central alarm unit located under your seat has gotten soaked. I think someone posted a method for drying it out that may restore function (try searching "wet alarm ").
More importantly, you need to determine why the footwells are wet. Most likely plugged drain tubes. Again, a search of the forum will tell you how to locate and clear them.
Good luck - post back if you need more help.
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'99 black 986
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