OK, at the expense of looking like a complete noob, which I am when it comes to kayaks, what is the advantage and drawbacks of having a spray skirt? Have read that they keep you warmer and dryer, very important in Spring and Fall kayaking, but what else

Hi Tom,I was a noob not so long ago, & still have reverting tendencies.
A spray skirt makes a big difference to your comfort where drips don't get to annoy you and sunburn wont get your legs, so much.Swamping is also averted .Rolling is normally optional but getting the spray skirt off is simple upside down so not a biggie.You will have practiced getting it off, up the right way ,many times before you find yourself in that "unfortunate" position.
You will look like a wally if you walk around with the spray skirt on but that's not too bad a drawback?

The weakness in the deck created by the "noob" that put the hole in there in the first place can be made good by constructing the coming riser and lip which makes it a good idea anyway just to beef it up.

Your irregular shaped hole needs to be addressed but it's no biggie,if the outside of the lip is good the spray skirt [they stretch heaps] will cover up any misshapes if you can't get it right.I would suggest a flatter back anyway as you will find, as is, will pinch you if/when you lean back. If the hole is too big then the combing riser could be made inside the hole rather than laminating ply on top and outside the hole.All this is work and effort but it's worth it, I think.

The first photo in your post looks to me like a normal, spray skirt fitting, combing made from carbon fiber I guess?
I hope this helps with your confidence to proceed and you get the bug to keep going with it.
Cheers from Paul.