h'okay, well, a big issue is that you arn't using the same colors, I suggest you do. in some cases, such as the grate along the floor under the scorpion, you but some tilework, while its suppost to be... grates, make you sure you correctly identify what a texture is before replacing. Also are you using overlay textures? its easier to take the original texture, and add overlays to it than take 3rd party textures and put them in, (thats what it looks like for your tiles)
Also on the bridge infront of the reactor... squaresoft fail for epic texture misalignment ><