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hello, hope this can help, I already built 3 kayaks, using routered half lap joints on my side panels, easy to do and to align when it`s time to glue them together,
the way , i do it, I simply route away 1.25 inch on the whole end edge of 2 panels, flat, flip one over, and glue them , the alignement is perfect
the rest is usual business.
of course, the adjustement of the router must be exactly set, which you achieve with scrap wood, and patience.

John, Montreal

good luck with your project