It is staying running because the alternator is still energized. You should just be able to hook up the Check and Choke Relay.
That B/W supplies power to alt/CCR; auto trans; coils; F/P: nearly every circuit in the vehicle.
Check out the W-1 page of the wiring diagram. It shows where all the main wires go and shows where to look if you are having odd problems. Many circuits can be affected by something wrong in a different circuit. Very rare I remember 4 I have seen, two human caused, one corrosion in wiring harness and one packrat.
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