Silencer alarm system uninstall

Thank you InkJunkie for the schematics.
I'll post an updated pic just to show all I did with the security system is connect the yellow wire and disconnect the splice connectors.

From what I can tell I don't think there was an issue with the security system (I think). I have been reading other people that have had this issue and it got me thinking about recent issues I was having with my ignition switch. The switch never has wanted to turn back to the accessory and sometimes gotten stuck in the on position (2), could this lead to similar issues I'm having?