I'm copying what was there because friends at Rockport marine advised the same method.

Which is to mill a piece between the well sole and well sides. They call that piece a 'grub'. It frames the sole decking and also raises the sole decking line up so varnish or paint won't be constantly immersed. It's a trouble area. But it means you trust the decking and caulking to be water tight.

My grub will be 1" high with a cove shape between well and 1/2" above the decking. One of the last things I'll do is epoxy(thickened)and fasten the finished sole to the cockpit well sides before installation.

I will epoxy all the cut outs, good idea. All this stuff is easy as the finish isn't important(like on the well sides). I just bought a gallon of west and fast hardener, I think most of this work will be done before it warms up much.