This will be a fine exercise before building your own boat.

A few options; all glass coaming, ply/glass coaming, or all wood.
Check out www.oneoceankayaks.com for ideas about making a glass coaming.

I'd remove all of the old coaming and make a template on the existing coaming riser/spacer. Get a piece of cardboard and make a template using 1/2 of the coaming with the asumption a mirror image will work otherwise make two halves by laying cardboard on the spacer and running a pencil along the inside. Add 1" on that curve for the outside dimension of the coaming.

Good 1/4" ply should would be fine with plenty of rounding over on the inside edge. You don't need Okoume if it's 6mm,1/4" Most likely the builder didn't seal the original wood well on the edge. When you round it over build up four coats of epoxy with the understanding you'll probably sand through two. If you went with 4mm then Okoume or similar ply is worthwhile.

If this is the same kayak mentioned in the CLC forum it sounds a little like a Cape Charles where two strips of wood were used underneath the deck for the hatches,,and you're right, it's inadequate. Put reinforcement on all sides of the hole and on the aft hatch put another transverse strip along the forward edge of the hatch. If the person who glued them in only used clamps at the hatch hole then there was nothing clamping the strip to the deck near the sheer and there's probably air gaps. I was able to rip out strips like that on a couple original CLC kayaks because they weren't clamped beyond the hole.