Among other builds, I've built a Chess 17. Excellent kayak.
1. I did all my puzzle joints flat on the floor. Paint cans, tool boxes etc. on top of random wood boards for the weight. (I've never used the "Gatorade" method shown above - but whatever works!!") Don't use excessive amounts of epoxy on the puzzle joints, minimize the squeeze-out. I definitely recommend a table/tables for the remainder of the work. Saw horses can work, but don't give you a place to set things down. Nice heavy solid tables are great, but even two cheap plastic fold up tables from the box store work fine, store out of the way whenever needed, and have many post-contruction uses. I definetly recommend a "construction cradle" for the hull. Just random wood like a 2ft. long 2x6 board cut with a wide notch to create a two low-angle v-shapes, with a stable base nailed to it to set on the table. Cover the supporting edges with plastic. Place them at about 1/3 and 2/3 of the hull length. Works with moat right side up, upside down, and even holds boat at an angle with one side or the other rotated up for ease of work.
2. Of all the different seats I've used, I like the Creature Comfort - but there are oh so many options, and so many different derrieres that preference is very personal. I've left out the hip braces in all my kayaks. Just never felt the need for them. I've also done away with the "keyhole" shape, going for oval. Laszlo's coming hint above is something I'd do on my next build. I had no problem doing the coaming "per the book" - but was sure to use a gloved finger to smooth in a good epoxy filet under the coaming. I'm sure his method would save a cup of epoxy, and some sanding work.
3. I paddled my boat for about a year with no skeg or rudder. Then purchased a Windsail, which made installing a rudder a must-have. Now I like having the rudder even while not using the sail. It does add something that needs just a little extra care when moving the boat around on shore so as not to damage it while handling the boat, but no big deal. I would NOT consider a non-retractable skeg. So, I think that a retractable skeg or rudder isn't necessary, but I've read that many like the retractable skeg. But in my opinion if I was going to do a skeg, I'd just do a rudder instead. More functional options, about the same expense and extra effort to install as a skeg. And whatever you do, it is easier to do it during the initial build.
4. I've put my footbrace mount screws through the hull, but respect those that don't. If you do decide on a rudder, do take some time to read up on how to select the proper height so that your toes are in the right spot to control the steering pedals. Whatever you do, don't leave off some type of footbrace. Footbraces add much potential power to your paddling (says the guy without hip braces...). And everything about installing footbraces is easier before installing the deck - even though I didn't do it that way, I would if I did it again.
5. I would absolutely pull the stitch wires. Can't really imagine any good reason to leave them in. Filets will be much cleaner, smaller and easier with wires pulled. With 4 builds complete, on my last 2 I shifted to CA glue for tack "welds." So, so, so much simpler, faster, cleaner and less work. Did I mention cleaner and faster?! There are times when you might desire a dab of epoxy on a joint where you worry that high stress might pop the CA joint when you pull the wires prior to getting the filets done, but those are rare places. Pulling the wires actually saves time and work that you'll otherwise have to put into extra sanding.
Enoy the build and good luck.
Bubblehead
As Laszlo says, this boat tracks really well so no skeg needed. On the other hand, a skeg really helps when paddling in rough conditions and there are few negatives to adding during construction. I retro-fit the CLC kit which was a bit harder. 
The Ch17LT was my first build that still gets used for recreational paddling, especially for longer distances. I will be taking it on a week long kayak camping trip in the keys this coming January.