Here is the idiot-proof, accurate, and simple method I used to transfer the outline of the deck skeg trunk slot to the keel, without slop. I haven't figured out how to upload the photos, so if this is unclear, please instruct me in that and I'll post them. 

My project is the PAX 20, but this method will work for any build which requires the skeg trunk slots to be cut after the deck is installed. It's tough to work in the confined space under the deck, so marking, measuring and using tools in that space is problematic, at best.

Cutting the deck slot is straight forward, following the dimensions on the plans, and the width and length of the trunk. How to transfer its outline to the keel? Use a length of tape ( I used wide 3 M blue painter's tape) longer than the deck slot, and stick it inside the boat, lengthwise on the keel, under the deck slot. Lower the skeg trunk into the slot, onto the tape. Mark the bow edge of the trunk with a pencil. Remove the trunk. Turn the boat over, and drill a small hole in the keel ( I used a 1/8 inch bit) so that it will penetrate the tape somewhere along its length; it doesn't matter where, so long as it will be astern of the line you made on the tape, and within what will be the width of the slot. Remove the tape from inside the boat, and place it on the keel outside the boat, matching the hole in the keel with the hole in the tape. If your eyes are poor and the shop is dark, matching the holes is very easy if you put a light in the hull to highlight the two holes as you position the tape. You now have the exact position of the bow edge of the skeg trunk, transferred onto the tape on the outside keel. If your boat has a flat bottom, you can align the trunk's bow edge with the mark and trace its outline on the keel, without any measuring at all. My boat's bottom isn't flat, so I used an X Acto knife to cut through the mark on the tape, transferring it to the hull's epoxy layer. Take off the tape, and the mark is readily visible. Lay out the dimensions of the trunk on the keel, using the bow mark as a register. Use the X Acto knife; a pencil mark doesn't show well on epoxy. You now have the outline of the deck slot transferred to the keel. Cut out the trunk slot with a saber saw, and clean it up with a file and sandpaper. My trunk fits very tightly; there is no slop, and no gaps to fill with thickened epoxy. Works great.