96 ford contour problem

sorry if this is confusing at all, i just woke up and im kinda groggy yet. Our 96 contour has a problem where it wont start sometimes. heres the deal, I replaced the motor last year with a very low mileage one after the original one crapped out. Ever since replacing the motor, there would be a really bad idle which ended up being that the throttle cable would bind and the throttle would stick, if I twist the cable, the idle would go back to normal and the cable wouldnt bind. After finally getting the cable in a position that it wont bind as much, other idle and running problems started. I replaced the plugs and wires with oem ones and replaced the pcv valve. I then found that the engine wouldnt start and had no spark at all, it turned out that id broken the end off of the crank position sensor when i replaced the pcv valve. heres my main problem, every now and then, the car wont start and has no spark. Sometimes even after it starts and i go somewhere and shut it off for just a few minutes it wont start. i have to wait anywhere between a few minutes to several hours before it will even fire up. could it still have something to do with the crank position sensor? There seemed to be an elongated mounting hole in the sensor, does the sensor have to be aligned a certain way? ie twisted one way or the other? it doesnt seem to twist back and forth at all when i loosen the mounting screw though. or could something else be causing it? I also replaced the coil pack with a known good one to rule out the coils crapping out this is mainly my wifes car and she now refuses to drive it because shes afraid it wont start for her