THINGS TO WATCH FOR
hull or deck spread
This is one of those situations where some care up front can save a bunch of work, frustration, or a poorly crafted deck-to-hull seam. Once one side of the hull (or deck) has been glassed, there is a good chance it will change shape if left to it's own devices. Humidity changes is probably the primary culprit, but since resin shrinks as it cures, this might also be a cause. In any case preventing changes is fairly simple. One way is to cut spare strips to the same width as the forms and tape them in place with fiber tape. Another is to cut your forms (that have been removed) from shear to shear and tape the appropriate halve back in the hull or deck.
There are good reasons to avoid the problem even if you can force a good match. First, it's a bad idea to build stress into the wood if it will ever see hot weather. This can lead to visible stress marks in the glass matrix (see next section). Second, once cut out the hatches will resume their unstressed curve making for a poor fit with the forced curve of the deck. This is a very difficult thing to fix.
avoid stress flecks
Really what I'm suggesting is avoid building stress into the wood parts of your kayak. Stressed wood can shift slightly when hot (e.g. setting in the hot sun) resulting in raised edges between strips or white stress marks in the glass matrix. As mentioned above, forcing miss-matched kayak halves together is one cause. Another is forcing wood to bend or twist under a lot or resistance. A better way is to steam bend or use a heat gun (my preferred method) to coax the wood into position. If the piece is short enough, a microwave oven works wonders at making wood pliable as rubber.
hatch edge stains
One of the persistent problems with wood kayaks over time is staining around the hatch edges. These edges get abused yet don't have the glass layer protection like the rest of the deck. My solution is to round off the square edges and then build up a thick edge of resin thickened with fused silica (on both the hatch edge and the deck edge). One may have to sand the hatch slightly undersized in order to have room for the extra material. Building up thickness is a tedious fussy job, but will save repair work later on. Besides, once staining has set in, there's probably no reasonable way to fix it. I use small wedges of minicell foam to brush on the resin and then turn the hatch every few minutes. Once the resin starts to thicken, I may brush on more.
seat bolt holes
While repairing a cheek plate on a Pygmy Arctic Tern, I found that the seat bolt was elongating the hole in the wood support (cheek plate). The bolt threads were chewing their way through the wood when I pressed hard on the foot pegs (presumably from rolling practice). A metal bushing, aluminum tubing in my case, placed over the bolt and in the hole solved the problem.