Ok so I started over from scratch, since I found a few better ways to lay stuff out.

When I did a test compile it loaded up fine, but when I got in game, the Skybox is weird and has a seem, and All the walls seemed to do this weird shimmering effect where they vibrated weird.

What's the jig?

the seam in the skybox is just part of the texture. that's the default skybox and isn't used in HL2, it's just sort of a test skybox. you need to change it to a different one in the map properties to get rid of that.
as for the walls, i'm not sure what the problem is, but you might be used model textures on them, which causes some strange errors (model textures all start with props/....)

Ahhhh the skybox, you're right. Totally forgot to change that when I started over! Ta.

As for the weird shimmering, I only have one model in there, and that's the tiger.

he means u are using model textures on your brushes. change the textures to something else and see what happens.