Note1: I am totally new to this concept of re-skinning things, so sorry if im not making sense at all.

Note2: I'm having some issues when im changing the textures and files of minecraft. Right now im using SMP's Realistic texture pack, which I forgot to take off for the sake of this issue im having

Note 3: I dont intend to release any packs that use SMP's pack, as he requested in his post. 
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My issues:

Im trying to change the color of the water and the skybox to make it appear that the time of day is evening. What I got so far is pretty homely, but im getting used to it.

I replaced the water color to appear purplish, which it did outside the playable zone. However, as shown in CIRCLE B, the water in the playable zone didn't change colors. I used the water.png file that was found in the extracted minecraft.jar file which I downloaded from this site. (I followed SmokeyDB's Creating Custom Textures post) Im assuming either I missed another water file, or that it isn't possible to change the color of this type of water.

Finally, in CIRCLE A, There is the issue of the white foggy horizon. Is there a way to change the color of this?
 
Thanks. Sorry for the confusing post.