Battery re-wiring ???

Thanks for the pic's, I definitely was not envisioning anything like that. I like the way everything is protected in the electrical boxes.

Where did you get the bus bars from? In all my searching I never seen anything as simple as those.

Did you run a individual battery wire to each bus bar, or are they wired in a series? Power provided to the second junction box from the first box?

On mine one box is positive and the other is the negative box. Unless you have a ton of stuff a bus bar with spots to hook four or five lugs is about all one needs.
I got my bus bar from an electrical tech friend, he gave me 2 pieces of copper and 2 pieces of aluminum about 4"x 8". I cut one of the bars in half and trimmed the length to fit in the electrical box. 1/4 X 20 holes were then drilled and taped into the copper, spaced appropriately for the fuses I was going to use on the bus.
I had some nylon washers about 1/2" tall from Lowes that I epoxied to the bus bar then to the bottom of the box. The washers may not hold up in the box but all they were needed for is to keep the bar in place while I hooked up the wires. The bar is cut tight to fit in the box so once the wire are hooked up the bar isn't going anyplace even if the epoxied washer fail.
I purchase boxes with threaded holes in them but if I was going to do this again I would get boxes with no holes and just drill my own so I could space the holes out along the box height so I didn't have as much trouble keeping battery lugs from touching each other. Follow westend's link to fuses as the ones I purchased from my local radio install place were longer and made things really tight in my positive box.
For connections to the bus bar I used 1/4" x 20 x 3/4" stainless bolt's, lock washers and flat washers screwed into the taped bus bar holes. The same bolts where used with nuts for fuse to lug attachments.
My next step is to put a little tape around the wire entry holes inside the box then fill each hole from the outside with silicone to seal of these entry points.

In my pic the box on the left is positive, the right negative. I can see some confusion since I have red wires running into each box. I used a couple sets of 4ga jumper cables I had to wire my solar controller and inverter. The jumper cables have a ripped cover on one side and a smooth cover on the other, I used the ripped side for positive.

I bought bus bar from Discount steel. Holes are drilled and tapped in the bar. The copper bar is attached to pieces of HDPE I had around and those pieces are epoxied in place. I used standard weatherproof 4" utility boxes.

You need two bus bars if you are organizing both the positive and negative phases of the 12 V DC system. If your negative phase is split off to the frame and organized well, you only need one bus bar. Bus bars are also sold premade or a guy can buy a lug terminal strip to handle the connections.

Good luck with your project!