aside from the 2nd pic those are all just fuses, looks like most have no connection a couple them are spares for whatever you want to add.You would be 100% correct! I've put an ohm meter on the two large fuses on the + terminal of the auxiliary battery (Picture 1) and they both test ok. All wiring that you showed in your previous pictures looks ok. Where would the best place to start looking for that break in the main harness? I did notice that the Ignition Controlled Charging Relay is still installed and hooked up (Picture 2).
I also located this in the box mounted above the main battery. Is this (Pictures 3-5) where I need to start looking?
take note that if you happen to "blow" one of those "fuse" the entire assembly has to be replaced for the 1 fuse to work again as it is all one piece and runs about $100-120
I have done it already when I installed a bad amp and the amp smoked and blew the fuse with it.
the piece in the 2nd pic is the battery isolator for battery #2