Before I get started I just want to give a recommendation. Whenever you are putting hardware into a boat, make sure to use stainless steel hardware. You may pay a little extra for them but your money will be well spent. You won't have to worry about rusted bolts in five years when you go to change out something. I buy them in bulk and save all the extra stuff that comes with new products I order.
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Tonight started with the battery compartment. The main battery was too small. In this picture you will see the original configuration.
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Take note of the wire tunnel in the right corner of the photo.

Because I was putting in a size 30 battery, I needed to reconfigure the layout. I removed the old battery box and then removed the wire tunnel cover. This boat has alot of rivets and I drilled them out. Because the layout changed, I had to rethink the mounting of my charger. I mounted it on the bulkhead, scribbed the wire tunnel cover, cut it with a dremmel, and installed with stainless screws. I then put the new batter tray and battery in.
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When making my wire connections for my charger extension, I always utilize shrink tubing. I then overkill it buy taping the ends.
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After both sets of extensions were done, I attached to my fish tape and pulled them through to the trolling motor battery compartment. I terminated the ends with the required inline fuses, wrapped the wires in a protective casing, and installed in the battery boxes.