I think by putting the alt charging directly on the battery rather than following the stock route through the ammeter etc as 67Dart273 stated is the cause of your issues.
Thank you for the diagram as I think you are correct on how I am currently doing things but I don't see the difference on that diagram (how i'm doing it) and the photo in the 1st post.
Whole reason why I ran that 6Ga wire to the battery side of the switch was to pass NHRA regulations. Previously without that wire the car would still stay on when you disconnected the switch as the car would run off the power coming from the alternator.
It ultimately sounds like I may need to try to find a new way of disconnecting the alternator as I thought the first photo would accomplish that with no issues.
