MicD

Trying to figure out what these two boxes are for. The one with only three wires seems to affect the ability to start my jeep. The other has no affect on anything but has wires going everywhere.

tech

I would guess that they are after market parts maybe a alarm .

doublechaz

I was having an occasional no start and occasional alarm for no reason that could not be turned off with the fob in my Chrysler 300. Examination found something similar to your two boxes *really* poorly hacked into the under dash wiring in several places. Further research showed it was a GPS tracker, alarm, and ignition kill with cellphone connection. Cars are routinely butchered by the dealership to put this crap in so they can knock you off the road, locate and repo if you are late on a payment. Being second owner of the '09 300 I got it all out of there and did my best less than $500 restore to near factory work. No problems since, and no dealership or hackers are tracing my every move with that junk.

Your stuff may be something else, but if you can find numbers on it try a little google and see what happens.