Some of these are CSS questions and some are not. Many have been answered in the forum, as a search would show.

- How do I re-order pages other than alphabetically? For example, I want the HOME page to be at the left, while it is somewhere in the middle.
Use a custom menu.

- How do I associate categories with pages? For example, when I click the category I want a post to be under (when in the post screen), how do I get those posts to show up on certain pages?
Use a custom menu, again. Link the tabs to the category pages.

- Is there a way to have said posts be organized in a blog roll style? For example, on the home page I like that the posts show up in boxes that you click on for the entire post, but once I sync categories with pages, can I get the posts to appear in a standard blog style on these pages in descending order from most recent to less recent?
Use a theme that does this. Some do, some don't.

- How do I include the post author's name and thumbnail photo/organize the content below the post title when viewing the whole post?
Use a theme that does this. I think there are only 1 or 2 themes that display the author's gravatar automatically: otherwise, you'll have to upload it as an image.

- How do I replace the commenting section with a commenting section through Facebook?
Cannot be done at WordPress.com

- How do I make it possible to have certain pages at the top of the page, and others below the header?
Custom menu, again.

- Where do I change the color scheme of fonts? I know I can change the background color, but where do I change the color for post titles?
- How do I re-order pages other than alphabetically? For example, I want the HOME page to be at the left, while it is somewhere in the middle.
- How do I associate categories with pages? For example, when I click the category I want a post to be under (when in the post screen), how do I get those posts to show up on certain pages?
- Is there a way to have said posts be organized in a blog roll style? For example, on the home page I like that the posts show up in boxes that you click on for the entire post, but once I sync categories with pages, can I get the posts to appear in a standard blog style on these pages in descending order from most recent to less recent?
- How do I include the post author's name and thumbnail photo/organize the content below the post title when viewing the whole post?
- How do I replace the commenting section with a commenting section through Facebook?
- How do I make posts have a different background color than the main blog background color?
- How do I make it possible to have certain pages at the top of the page, and others below the header?

Any and all help is appreciated! Any CSS codes that help are welcomed as well!