The problem your trying to fix is two fold. First, your old wiring has connection and continuity problems. If the car was all stock electrically, a Year One harness might be a good start for a solution, but you still need to deal with the low amperage alternator output at idle issue, the amp gauge issue and the bulkhead connector issues that are inherant with Mopars.

Second, you've added significant additional electrical loads and put in a high-output alternator. You need to be wise when incorporating those add-ons into a well-sorted out "stock" electrical system that has had the above mentioned upgrades performed. They need to draw power from the correct location in your electrical system in order to not cause problems.

You can get away with piece mealing and adding on to the system as you go and hoping for the best, or do it right all in one shot from the ground up.