I've heard that this can be a tricky stitch-n-glue to build. In reading Nick's notes in the page that contains the offsets, it looks like the area of major concern is the bow and stern; "Once you have epoxied the hull it becomes very stiff, especially at the ends. You will not be able to adjust it to fit the deck." (quoting Nick) But in your case, you'll be custom-forming the deck to match the hull, so there will be less 'fighting' to get the 2 halves to meet.

I think there would be 2 key points to make regarding what you are proposing. One is that you should rig up a string and make sure the hull is well aligned; that there is no twist in it. You might want to take the form offsets, offset them 4mm for the wood thickness, and make a few cradles to hold the hull in the correct position. Another would be to stretch a tight string from bow to stern and line up the centerlines of each form to ensure the hull is straight. Normally if the boat were made as a stitch-n-glue, this wouldn't be necessary, because the deck helps force the hull into the correct shape when the 2 are stitched together. But in your case you'll need to ensure this straighness some other way.

The second point would be to not get too fancy with your stripping of the deck. The forms are 20" apart, as opposed to the usual 12" spacing for a strip kayak. You'll probably want to stick with a straight stripping pattern and just use different wood colors for variation.

Happy building!

Dean