-- Last Updated: Sep-24-12 9:03 AM EST --
Waves and large cockpit very stable boats don't go together well. Two parts -
As you found, large cockpits and waves create a heck of a good opportunity for a flooded boat.
"Very stable" boats generally mean a high degree of primary stability and a wide boat. Sea kayaks, intended to handle waves, are much narrower and are designed to be wiggly on flat water but take the angle of the face of a wave in stride and return to upright after the waves passes underneath them. It is a very different stability profile than a flat water boat, which tends to be much less adept in handling that situation.
As to handling the waves and paddling out of the problem, you need to edge into the face of a wave then can paddle over the top. But that requires a level of contact with the boat that you may not have because of the size of the cockpit. Your thighs or knees need to find some kind of surface to use to control the boat, that surface just plain may not be there in the craft you name.
A good set of float bags can reduce the amount of water you acquire, if you can find a way to anchor them securely in a large cockpit boat. I wouldn't count on that - waves are very good at taking things out of a boat unless the stuff is really well tacked down in there.
A skirt is easily challenged at stopping dumping waves at a certain size - the wave will collapse it. Most boats that are well suited for fishing have that scale of cockpit.
You will note that most fishing boats for bigger water are actually sit on tops - your experience today is the reason for that preference.
I just went back and confirmed the description on this boat. It is marketed by Dick's, as in the big box store, and has a 45" x 18" cockpit and is 29" wide. No bulkhead in front. Assuming I have the boat right, any skirt you get for this boat will cost a bunch and will not handle being dumped on by waves. 29" is not the widest glorified rec boat out there, but it is still several inches wider than a full out sea kayak.
Given that this all happened on the shoreline of a coast with at least one rock in it, I am guessing that your actual goal may be to do some paddling on the ocean. Or at least inland oceans like the Great Lakes. I suspect that you can find better places to get advice on that then Dick's. If you provide some information on what are you are in, folks here can probably suggest some good outfitters to go to about getting set up for salt water paddling.
In sum, don't spend any more money trying to make this boat into an open water/ocean boat if that is your goal - nothing you can add to it will ever turn it into that kind of boat. Enjoy it for what it is, on quiet flat water, and stash your cash for a more apt boat and learning how to use it.
Also, messing around in rocks and wearing a helmet should go together. If you don't have a helmet, don't go there.