Electrical issues

The previous owner installed an after market security system that has completely messed everything. They installed sub-woofers and amps and all kinds of other after market stuff as well. When they traded the truck they ripped most everything out, leaving wiring hanging everywhere. The security system remained installed in the vehicle, and was also equipped with an aftermarket remote start. When I first purchased the truck it ran fine. Now the turn signals have stopped working in the back, as well as the emergency flashers (The front works fine). The radio has also quit working and the interior lights as well as the exterior lights shut on and off periodically, as if there is a short or a live wire somewhere. I am fairly decent with electrical, and have checked the fuses (none have blown). I have pulled probably fifty feet of non-essential wiring (Wiring that was just hanging and not attached to anything) from the vehicle. I was told it could be a bad ECM, but other than the issues I have stated the truck runs like a champ. There are no engine issues whatsoever. I have also replaced the turn signal switch, thinking that it may have been going bad. I have a few ideas on what it may be, but could use some help pointing me in the right direction. Any ideas?