if it was a standard aftermarket alarm that was put in like normal the NO there is not a kill switch that would do this, the normal alarm goes to a relay that interupts the power from going to your starter relay/solenoid. If someone got in to the wiring and added a totally custom rig then you may have a kill for the fuel pump, but to kill spark that would be ballsy since any extra wire in the signal path could pickup or emit rf interferance ( the whinny noise in an old radio due to older systems not being sheilded).

as for color of wire it could be anything since what your talking about would be totally custom. also you would have probably noticed if you flipped a switch that you didn't know what it was hooked to. these are probably 2 unrelated problems that just happened together.

what type of alarm was it? and about how old?