Basically, you need either the positive or the negative connection to the battery bank to be at the far side, and the other one to be at the near side, and only one of each. You can achieve that in a few ways: by using a long wire to connect the far side ground connection to the current near side ground (via the shunt), by using a long wire to connect the far side positive to the near side positive stuff, or by making the ground connection for the batteries at the far side (via the shunt). It seems to me the last option is the simplest, and requires only lengthening the sense wires to the shunt and finding or making a good ground connection on the far side.