I don't think remaking the whole deck would be the route I would want to go down as I have completed the deck, including the coaming

Just in case you didn’t quite get the simple remedy I was referring to:

by tipping up the recess horizontal's ends of the forward short recess strips, you could actually re-achieve the original cross sectional shape of that kayak at the front of the ckpt while still retaining the desirable dropped rear. Redoing this and the upstand would probably only take an evening or two - and you could achieve any clearance between what you presently have and what it originally was designed for even without the recess. Heck, if one wanted to get weird, the coaming could be raised inches above the deck – it just depends and what angle one wishes to tip the ‘recess’ strips.

These schematics may tell the story. You can see in the lower schematic, that the front of the ‘recess’ isn’t much of a recess anymore – just due to tipping a few strips. (Note if you reuse the strips, the ckpt will get a bit larger, but that’s your call):