I'm not sure I follow your problem. Most kayaks have curved coamings following the line of the deck. There is no problem with cutting the coaming riser at a certain depth from the deck all around (about 1"). I have a coaming recess, so it was flat across the boat, but it curved down to the middle, up to the ends, as yours seems to. The coaming then follows the line of the boat and looks quite good. I have never had trouble with the skirt (neoprene) not fitting or leaking.
However, if the deck goes up from the sides to the centre line you will end up with a peak in your back and that will be uncomfortable. You might want to vary the height of the riser around the back so as to avoid that, or else recess it. You can still do that easily at this stage.
JohnK

: Well I think I make another mistake. Got my coaming fitted and realized that
: I forgot to put a mockup of the cockpit on the frames so my deck was not
: flat at the coaming. Leaving the sides higher than the front and back of
: the coaming.

: Am I correct that lowering the sides, so that the top of the coaming is not
: flat, would be a mistake? Or should I just mark it off and trim it? Most
: the time I will just be using a nylon skirt. I don't expect to roll this
: boat but you never know.

: I am clamped on a strip for the lip I was planning on using, but it's to big
: (looks wise). I am going to make it thinner so I can lower the coaming
: some.

: All that to say, Got any advice??