James,

For the time being, get some 1/8 inch thick gasket tape from Newfound Woodworks (http://www.newfound.com/). It compresses very well. To compress it even further, make the gasket narrower by splitting it lengthwise.

Later you can remove the hatch lip and build a new one using a spacer (of 1/8 birch ply or the like) so that your hatches are flush with your chosen gasket material. I rebuilt one of my Pygmy boats just that way and it works fine.

Ted