Your posture will not be the same for paddling as for rowing. While your rowing machine frame has footpegs, which should serve you nicely, remember that a kayak seat has a back support. If you don't keep your back supported on your trainer in the smae amnner that youw ould do so in a real kayak, then you may find that you try to "paddle" by rhythmically moving back and forth at the hips. In effect it would be a mix of a paddle effort and a rowing effort. Who knows if that mix of movements would actually help you.
Why not just park the kayak facing a wall and mount your exercise equipment to the wall alongside the bow? You could take advantage of a rounded hull to allow you to tilt and sway a bit. Mount a shelf on the wall right above the bow and install a TV. Play some videos of sea movies and you might feel like you are out on the ocean. 
PGJ
PGJ
