Rear bulkheads are less of a problem, since there is less advantage to moving it. However, if you look at some of the well-made kayaks with curved and sloped rear bulkheads, you'll realize the advantage of an easy-to-drain cockpit. Using pretty much the same techniques as you would for making a new forward bulkhead, you can replace the rear one.
First of all, decide whether you want to keep the footpegs and rails you currently have.
Rudder?ed kayaks are slightly more problematic, since moving the bulkhead means moving the [sliding rails]? and ensuring there is still enough room for them to work. This is a good time to replace the sliders with fixed position, gas-pedal-type footpegs. These can be fitted into a tighter space as they do not require room to slide.
Rudderless kayaks have footpegs that can be removed entirely. You can position the bulkhead so that you place your feet directly on the bulkhead for bracing. This means that the footpegs and rails are superflous and you get rid of that weight. If you choose this route, remember a few things:
Once you decide on how you will deal with footpegs and location, cut out the existing bulkhead. It likely can't be used again, so don't worry to much about trashing it in the process.
To get the shape of the new bulkhead, use a flexible rule, heavy, stiff wire or other means to get the shape. Pressing a stiff wire around the inside of the kayak at the position of the new bulkhead will allow you to transfer the shape to a large piece of cardboard. When you think you've got a fair idea of the shape, cut out the cardboard and see how it fits in the kayak. Without a doubt, you'll need to make a few adjustments.
You have to decide as well how tight you want the new bulkhead to be. A very rigid bulkhead tight to the hull can make a stress point in the hull. Some paddlers prefer to leave a tiny gap around a stiff bulkhead and fill the gap with sealer. Others will build up a fillet of fiberglass or Kevlar tape in such a way that it has some flex to it. Remember that if you are using the bulkhead for bracing, you will need a strong connection between the bulkhead and the hull. You can have flex and strength, but that takes planning.
Bulkheads can be made of:
Now that you have the proper size and have chosen the appropriate material, cut the bulkhead to fit. Then use fiberglass tape, sealant or whatever other means is appropriate for your choice. Working with the kayak overhead and standing with your head and shoulders inside the cockpit is probably the most convenient. Remove the seat to make more headroom.
If you need to move the footpeg rail, it's as simple as drilling new holes for the new position and filling the old holes. A brad-point drill bit makes a nice, clean hole. You can close the old hole by placing a patch of fiberglass or Kevlar on the inside of the hole and, once cured, cover the outside with a bit of gelcoat.