Sounds like you have half figured it out mate. Dont be shy to rip out the rubbish. If you have traced the offending wires then take them out and re-run a good wire where it needs to go to the cranking battery.
You dont really need an isolator between the batteries but it is nice to be able to isolate them. Your Alternator should be able to keep up as long as your not drawing a ridiculous amount from accessories.
Your Voltage Drop at the back could easily and will likely be due to either a supply wire that is too small from the battery to the back or a bad earth at the back. 12v needs good size wire to supply to the back. Classic Voltage drop. Go and buy some good size wire and run it along the chassis rail then up through the floor and put a new plug on it.
If in doubt hook the new wire to the battery with enough wire to reach the back, add a plug to the end of the wire and sitting in the driveway plug the fridge inIf you have enough Volts the your on tap mate. unplug, remove the plug and run the wire to the back. Dont be shy though bud
it aint that hard.