Hm...i had a problem like this with the 02 Focus, random things worked and other things didnt, nothing running on the same fuses or relays, no head or brake lights, but had running lights, no front wipers but the back one worked, no heater but the back defrost worked, locks worked but not windows, very random, after going to like 6 places a local shop blamed it on the gauge cluster and wanted $50, well worth it, they took the cluster out and played with it, i got the car back and everything worked

99 Contour LX MTX, Cone Air Filter, Custom Grille 95 Neon ATX Intake, Ractive Muffler, Green Painted valve cover, fuel rail, and intake, b/w painted interior, white exterior trim, shaded tail lights