Large is relative. You will need to consider the width of the boat and whether you wish to put in a cockpit recess. Various companies including mine, include several cockpit sizes with each set of plans and I'm sure that others have options available. Talk to the designer and find out options.

A medium size from my research would be around 30-32 long by 15-16 wide (not including coaming recess width). Making a cockpit longer will lower the front area of the deck, since you extend into the lowering portion. When you lengthen a cockpit, you might need to consider the center of bouyancy and center of gravity as specified by the designer. If you shift weight forward or back by even an inch or so, it could affect the handling of the kayak.

You can simply adjust the size that you have in your plans. Trace out part of the pattern and then move the pattern forward to make it longer. As for spray skirts, most skirts come in small, medium and large and each will fit over a range of sizes. Neoprene will stretch more than nylon and all have adjustable straps around the coaming to pull tight. For example, my spray skirt fits very tight over my larger cockpits, (33 by 17) and a little more loose over the medium (31 by 16), but within acceptable range for recreational paddling. Personally, I would not worry too much about the spray skirt but make the cockpit what size you need and then find a spray skirt to fit.