just incase, you do know the green-yellow/yellow-black are switched / continous power? if you don't connect them both, it will only work when your key is in the ignition.
it shouldn't be affecting your doors or anything, because the wiring for all that is under the steering column and ****... unless you actually spliced the damn wires from under the dash.. that shouldn't be happening... and if you did - ****ty
goto walmart and buy the $8 wiring harness for 95-97 ford's
it will even say on that new harness of yours what each wire is, then go here:
http://www.the12volt.com/installbay/...31&type=Stereo