It's not uncommon to pad out the contact area with foam. In whitewater boats they provide padded adjustable thigh braces, but in rec boats you're left to do it on your own. Make sure you use closed minicell foam or else it soaks up water and starts to stink.
http://www.kayakoutfitting.com/
Above is a source of outfitting foam, but once you know what you're looking for you can also find it on ebay or sometimes locally.
Use DAP Weldwood contact cement in the RED can (not the green one) to stick the foam in.
I've installed drain plugs in my rec boats. It makes it a lot easier to empty them than just dumping out the cockpit.
http://www.campmor.com/sea-lect-desi...gpa=pla&ci_kw=
Once you've been paddling a bit you'll probably want a spray skirt, but for starting in warm weather and calm water you should be okay.
Enjoy the new boat.
Steve Z