Hi Elk;

The cockpit area will be reinforced with more wood & glass than probably exists in any other part of your kayak. You will place extra glass around the cockpit area, both above and below depending on your design specs, and you have all the reinforcements that will lend a lot of longitudinal stiffness as well as lateral strength coming from the coaming and its glass layup. It gets very rigid in this area, as I'm finding out (This is what I'm working on now).

I suspect most of us end up with thinner stripping when fairing around the cockpit, just be sure you have enough glass to distribute the stresses around a decent sized area. When smoothing the inside of the deck for glassing, if there are one or two low (thin) strips it would probably be preferable to fill those low areas with epoxy and microballoons as opposed to thinning the entire deck further, just to get it flat enough for glassing. The resulting cured epoxy-microballoon mix will have structural properties better than (i.e.) cedar anyway, and they can't be seen.

Best Regards, Spidey