These batteries are somewhat notorious for being "just enough". If you pull over for 5 minutes and don't turn off the key/lights, it could be enough to discharge it and not allow it to restart. Having said that, cut/open wires are never a good thing and I agree that you should see about removing excess and possibly repair the main harness.
Near the tail section, under the radio bracket, there are several connections for the right hand switches and over mirror harnesses. I would start by disconnecting anything there (I believe it is 4 connectors). I don't have a picture handy since we had the site server crash recently, but it looks kind of like a softer plastic amber bell about 3" in diameter. Everything in there you should be able to unplug as it is not part of the "normal" harness (it is all additional wiring for the PA). This *SHOULD* disconnect any added accessories that run off the right hand switches. I say should, because if they hacked into a power wire somewhere else, you won't know unless you pull all the plastics and check for voltage on the cut wires.
After that, I would charge up your battery and see if it starts, once it starts I would verify voltage output ~13.5-14.5 to make sure you have a working alternator and then go from there. You might just have a weak battery.
Good luck! I am happy to provide pictures if needed, but there will be a delay.
Ryan