(don't know if you've done it)

as this pattern is to related to the simple strong lines of a yak, it would be a good idea to print out your pattern at some easy scale and superimpose it on a dwg/pic of a yak and the cockpit/recess layout.

that may give you some better cues on how/whether the pattern should stay the same width all along the changing boatwidth, how/where it starts/ends, and also how it resolves/ends/splays/cuts at and from the cockpit/recess etc.

and as a construction method, i would strongly consider double cutting the veneer by hand right on the yak. then all the cuts will be perfect, tight and tracing is eliminated. at the very least maybe you can just score the wood surface with your machine (to get the pattern) and then use that as a blade guide for the double cutting.

quite a few pple here have used onlays (without inlaying) with good effect. check the archives to see if that is acceptable enough and then all winter can be used for that 2nd yak.