As a means of isolating the problem, can you swap the batteries, ie make 2 number 1, and vice versa? If you do that, and the current 2 in the 1 place now gets charged, and the current 1 put into the 2 place loses it’s charge, then that would seem to indicate that the problem is the wiring, not...
Seems like if you physically disconnected the back battery cables from the battery, and then if you boat still worked (ie radio runs, starts, etc) that would confirm that the front batteries are wired into the boat system. Probably easier than tracing wires.
Your cross beams are 102”, or 8.5’...which is the width of the boat. Gonna be a tight fit. My Hewitt lift is sized for a 120” clear width, so I would suggest making those beams longer.
I would also go with the longer bunk boards.