Quark must have a way to set the offset/scale/rotation of textures on a surface. Just set them all to 1 for scale and 0 for offset and rotation (except the stuff you've specifically aligned) and you should be good. Also, the grass/dirt transition texture needs to be aligned on a lot of stuff -- it only has the grass on the bottom on most of them and a hard edge where the dirt meets the grass on top.
Now that you've got a sky with a sun in it, you should use arghrad's sun lighting. I have angles for different skies posted here:
http://digitalpaint.planetquake.gamespy.com/testwiki1/pb2wiki.php?word=Sun+AnglesYou probably want to give it a
slight orange tint since it's a sunset sky. Don't go overboard. I'd make a small map just to test with to get the lighting right before you mess with it on your main map.
I'm going to see if I can run quark and figure out how to fix the texture alignment. It's easy to do in bsp -- you can just select by texture and apply new textures to everything. I don't know that quark has that functionality, though, so you may be stuck fixing each face manually.