I'ts impossible to read those. Can you post a line to download them, or figure a way to post them higher rez?
Something Francis doesn't cover is the unique Mopar ignition switch. IGN1 "run" (blue) goes DEAD with the key twisted to start. Normally the IGN2 (usually brown) is the ballast resistor bypass and the key switch shoots full 12V to the coil+. So you need to connect those two together and use that for your "run" line
BUT FURTHER and this has nothing to do with Francis. Often the blue "run" line suffers voltage drop. Some of this is the bulkhead connector--which I guess you've eliminated, and part of it is the ammeter circuit which you may have eliminated. But SOME of it is the ignition switch and connector Drop on this line cases the VR to OVER charge because the VR IGN terminal is receiveing reduced voltage, and ramps up the regulator to compensate
Cut loos the loads off the blue line in the engine bay. Use the key end of the blue to trigger a Bosch relay, feed the relay off the starter relay "big stud" through a fuse/ breaker, and connect the engine bay end of the blue to the load contact on the relay. You can also put a "not" obvious switch in the relay coil line to serve as a simple anti theft