Battery in Trunk wiring completed, now no power at all

Your car will not shut off by disconnect with that wiring. Tha alternator will continue to drive the system.
OOPs I'm wrong. With the 1-wire it will work.

But in your drawing,the battery and alternator are still "live", and a short on the cable can still set your car on fire. The disconnect needs to be the first connection to the B+, and they should both be mounted between the frame-rails, for maximum protection from a side impact..
All you need to do is; remove the battery+ wire from the Ford relay "s" terminal, and put it on the supply side of the disconnect. Then, as to the jumper that goes from the "s" terminal to the disconnect; remove it from the disconnect and reattach it to the big stud on the Mopar relay, Now you are in business.
The battery+ should go directly to the disconnect and nowhere else.From the disconnect it should go to the front of the car to distributed there.You could bring it to the ford relay and use the stud there is a jumping off place.
For the Ammeter to work, it has to be connected to the battery on one side and to the alternator on the other.Some of us have opted not to carry the high current thru the bulkhead connector, and no longer use the ammeter.

Having said all that, your circuit,as shown, should function, if the grounds return to the battery. Since nothing works, I would suspect the connection closest to the Battery negative terminal.