It sounds like all you really need to figure out is how to mount your Pelican box. It's pretty easy, just use an angle gauge (Home Depot has them) to figure out the angle of your hull, then use some plastic of an appropriate width, thickness, and length, as a spacer from your topside to being level with or just above your crown and bolt through using some 5200 or the like.
However, if your installing a battery box, you might want to think about mounting it inside the yak, to as you stated, keep the center of gravity low.
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