Speaking as the maintainer of the water code:
Seems like you managed to fix the weird inverted normal Issue I had which made specular wrong and I never bothered to fix. By this point I expect you have noticed I'm using real reflections for the skybox and distorting a transparent "reflection map" for objects that are near.
FYI the "artifacts" when you orient the wind north are dependent on graphic cards. It never happened for me on Intel GMA and I could never fix it because of that.
Make sure to test your code with all textures types and all waviness settings as there is a lot of room for mistakes there.
Likewise, the Red color that appears at low angle is WorkingAsDesigned and is there because of the distortion code. With the shader tries to get refraction texels that are "above water" pixel and contain garbage data. I detected this in the shader by checking the red component against the other one (the "horrible hack") and choosing the original undistorted texel in this case. However in some cases even that is insufficient. SO if you just remove the hack you're only going to break it further.
The red comes from the C++ code, the refraction texture is cleared with (255,0,0) before drawing the refraction. So when you fetch a pixel that's not rendered (above water) you get full red, which is why it happens on the edges of the map.
The proper fix for that problem is not trivial.
Also FYI the shore waves took me months of thinking to get somewhat right. I do not believe they are recomputed every frame, though, if they are it's an insane bug on my part. IIRC I create polygons by trying to follow the shore, but I never got it to work really well.
Edit: Oh yeah also I see you removed my comment about reflections being wrong at low angles far away, but the problem is still there. Just as an FYI, I still believe my "default to sky color" is the right way to go about this, but there is one thing to notice: since the normal map gets entirely blurry, the normal of the water plane becomes (0,1,0) ie straight vertical. But in real-life, you see the sky more because of the wave ripples. See my attached diagram. So that may be another thing to go after.