Do this first. Take the wire(s) off alternator #2's negative terminal and tape them up. Run a test wire from alternator #2's negative terminal to the negative post on the rear battery. Verify the large wire connected to the positive terminal on alternator #2 goes to the rear battery positive post. Once you have the wires connected to the positive and negative terminals on alternator #2, you should see 12 volts across them.
Start the truck and see if it charges. Ignore the idiot lights on the dash and check the voltage on each battery. If it doesn't charge, do
this.
Since the wiring has been changed, you will need to draw a diagram of where each wire goes and post it. It's impossible to tell from a picture of one end of the wire when the colors are different. Don't worry about the regulator wires for now. Take the big wad of electrical tape off the wire on alternator #2, you can't tell what is connected there. It looks like there are two wires on the negative terminal on alternator #2, are there? My truck only has one, where do they go? Take a picture of the batteries.