Oh boy, looks like you might be in for a wiring nightmare. Here's what I'd do. Get an accurate schematic, rip out the alarm system (there's no remotes anyway, right?), and put everything back to stock specs. This way you can start from scratch and know everything's working properly first. This'll take a lot of time & patience, but I think it's the best way in the long run. The instrument panel will have to come out, and you'll probably have to rerun some wires, so make sure you have a soldering iron and heatshrink nearby. Off hand, it looks like somebody crossed wires for the headlight switch and the fuel pump relay. Not cool.
If you don't wanna do it yourself, go to a reputable shop, but be prepared to dish out some major $$$. Good luck!
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Capri306, Moderator, The Mustang Works Online
1979 Mercury Capri, 5.0L -- C4 -- 2.73
1987 Mustang LX Notch 