Re: put my ducks in a row, please?
I don't know if you need to replace the transom or not, but if you do and you have to separate the top half of the boat remember this very important detail.
1. Cut away about 2' of the aft floor and then separate the top from the bottom.
2. Replace the transom
3. Put the top back on
4. Finish the rest of the floor.
If you have already removed the floor, then finish it up 2 feet short of the transom.
If you separate the two halves and rebuild the floor with the top half off, you will probably have to wrestle to get the top to fit back on correctly.
As far as your wiring goes, I wouldn't put it under the floor because of future access needs. Can you run the wiring under the gunwale? Either put in hoops to harness it or install a piece of PVC under the gunwale to run it. If you must put it in the floor, I would definately put in a piece of PVC and run it under the floor and seal it at both ends where it comes thru the floor.
Now as far as your list:
Personally I would,
1. Get the motor off. Take lots of pictures with your digital camera of how the wiring is run, carbs are connected, etc. Continue to do this as you tear down. You'll thank yourself when you re-install. Also, get a bunch of ziplock bags and a sharpie marker and put your bolts and nuts in them. This will save you lots of grief later on. You can then work on the engine and boat in parallel. This will give you something to do while you're waiting for poly to cure or paint to dry. Also gives you a little variety in case you get sick of sanding, at least you can get something done.
2. Flip the boat over and prepare then paint the bottom side with anti-fouling paint (Provided that the boat is small enough) You can also use this time while the boat is off the trailer to perform any trailer maintenance.
Once the boat is right side up I would
3. put in a new floor (You can do this first if you wish. I would do it after because I would want my new floor to cure completely before I started flipping the boat over and putting stress on my new floor job with the boat upside down.
4. paint the topside
7. new steering wheel, steering cable, and keyway (I moved this ahead of the wiring because of the rigidity of the steering cable. I think it would be best to have this cable finished before the wiring so that you don't foul up your new wiring job while installing the cable. They should both run up the starboard gunwale. (Provided you have a starboard console.)
6. wiring
7. guages
8. Install all of your hardware (Rails, cleats, bow eyes)
9. new carpet and interior - do this last because if you are still working you're going to have greasy tools all over the place. An uncarpeted floor is the best place to leave that stuff so that it is not sitting topside on your fresh paint.
10. make new canvas bikini tops (definately leave this till last. That may be next years winter project)