The thing I never see mentioned in these camper shell buildups is the bed length. Your Ranger bed is only 6' long, and if you are close to or over 5'-6" or so, your feet are going to be overhanging whatever platform you build inside the bed. You really want to be able to sleep on your stomach, so your feet are going to want to be extended "tippi-toe" out, making you taller, and also keep in mind that you aren't going to want to sleep with your head right up against the front of the bed or the tailgate.
I have been thinking about this a lot, and I think there are two practical paths:
1. If you are determined to use a camper shell, I suggest augmenting it with one of those truck tents that set up behind the truck and connect to it via a sort of sleeve that attaches around the open tailgate and camper shell back window. The ones I've seen permit the sleeve to be disconnected from the truck and zippered closed so that the tent portion remain set up and you can drive the truck away for sightseeing, going to the grocery or out to dinner, or, in your case, hauling the Kayak or boat to the launch site. I envision a sheet of plywood to "smooth out" all of the ribs of the bed floor for comfortable sleeping, with a hinged flap that extends the plywood "bed" over the tailgate to lengthen the sleeping platform out to the end of the open tailgate. In this case the Kayak could be carried on top of the camper shell.
2. Utilize one of those tents (a Sportz bed tent or similar) that actually set up on top of the pickup bed. Again the truck bed would be provided with a plywood floor with the hinged flap as I described above.
Option #1 actually makes the most sense to me, as by sleeping directly on the bed floor you maximize headroom in the camper shell so that you could at least sit up in "bed". Also having the tent "addition" means that you could unload your gear into the tent, leaving you with a lot more space in the "bedroom". Plus, as I said, you could leave your campsite set up with your "stuff" inside the tent if you need to drive your truck somewhere.
I don't really think you can get away from hauling your kayak on top of the camper shell, assuming your kayak is more than 8' long or so. Remember the bed is only 6' long.