1)I want to add pages not associated with the cart created with my own html/css.
See ez pages
2) I don't like the layout of the cart and want to change the content page and some boxes. Actually i really don't like the layout.
With some php you can extend it as you want
3) I wanted the categories box to go and I want the content page to list these like I see on most websites of this nature.
You have not defined what you see on most web sites, but if you want an unordered list(css) see this link and the apple zen template Here