I did it this way. As long as you run strapping (or similar) tape along the edge of the hull BEFORE stripping the deck so that the deck doesn't get glued to the hull it works great.

Order I used: strip hull, tape edge, strip deck, sand deck, epoxy/glass deck, take deck off forms, scrape/sand back of deck, epoxy/glass back of deck, sand hull, epoxy/glass hull, take hull off forms, scrape/sand back of hull, epoxy/glass back of hull (be sure to put spreaders in to keep hull width same as it was on forms), cut hatches and cockpit, join hull and deck taping inside, tape outside seam, sand/feather seam, build up filler epoxy coats on hull and deck, sand hull/deck, varnish.

I used this order on one kayak, a slightly different order on the other. As long as you put spreaders in the hull and deck when they are off the forms to keep their widths from getting out of whack you are okay with just about any order. You want to minimize the amount of time that epoxy/glass is on only one side of the hull or deck since having one side epoxied and the other raw is the most dangerous time for uneven drying and warping! I cannot stress enough the importance of putting temporary spreaders in whenever the hull or deck are off the forms and just sitting - once their width gets out of whack it is a real pain to join the hull and deck (which is already enough of a pain since you have to reach way up inside.

Having the hatches and cockpit cut out before joining gives you places to reach inside to tape the inside seam (the only part of the project that was really icky work and no fun at all).

As long as you take things one step at a time and think 3 steps ahead you will be fine!