I wouldn't even place a texture on water objects, Rem. They don't appear to 'do' anything for effect and cruising about some of the original levels, a good portion of the water objects aren't textured either. I can't see a difference --
*had the clouds in a test level too. They looked cool hanging against the slopes of the crater, though I think they should be omitted in areas directly above crater. The intersection with the terrain kills the look in area players can reach. I also reverted back to the tc.sky (you might have noticed). The sky model textures you uploaded a while back look quite good, but the horizon doesn't. No matter the fog color, you can see the edges of the sky where it ends (1000 ft up, i think) and it looked quite unnatural. Think the tc.sky texture worked out so well because the color so closely matched the white/gray haze of the clipping background and the clouds in that texture itself are away from the edges of the texture and more towards the center so it blends well into the dead horizon.
btw, here's the terrain file:
http://www.trespasserextras.com/terrainx2.ZIP
I didn't touch any of your riverbed work, (nice work on that, btw)but a small piece at the bridge to get a better fit for that model. Other variations are just small touchups along the bottom part of the path towards our lighthouse, as well as getting rid of some of that mushy terrain.