Here is my shot at an explanation.
From the baffle/pick up tube, res and on go to the res and on ports on the shut off valve. Out from the valve goes to the in side of the water seperator/filter. Out from the seperator/filter then goes to the supply on the carb. The return from the carb goes to the return port on the baffle. I would not worry about the vent lines. I did change my vent lines from the baffle to the T fitting, but left the rest.
Hope this helps, I am writing this from memory.