Battery in Trunk Wiring That Exceeds NHRA Requirements

Doesn't matter which side the battery cables are on those relays as long as they are consistent.

I do mine with the battery side to the rear and forward to the alternator and starter on front because it makes sense from a visual standpoint.

The jump wire on the CD relay MUST jump to the battery side of the Ford relay.

You could criss-cross the cables on the top relay and nothing would change the function of the system.

If you still have the black OEM charge wire attached at the alternator, that may be the issue.

You don't have the battery and alternator isolated from the rest of the system if it continues to run when the disconnect its thrown.

Also, there is no image of what you did in the post, just an IMG tag