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Below is the Ford diagram.
So far it sounds like you have more wires than the factory specs ( I have a large and small red and black wire. A small red wire and another large one that has a black and yellow wire.)
You need to test each wire you have to see where they go. You should be able to OHM test a Red wire to the starter and voltage test one to the batteries. You should be able to voltage test another to the ignition which will only show power while trying to start. You may also have a ground wire to the relay chassis that goes to vehicle chassis ground and you should be able to OHM test it as well.
Often there is more than one wire o n the battery post at the relay so other circuits can be powered from this connection.