Both will require some tweaks to the layout (Which it looks like you've already done some to get the menu list at the top).

To remove the menu from the side of your pages, in your Advanced LAyout, where you have

<!--System:Menus:Left--> and <!--System:Menus:Right-->


You'll want to change it to <!--System:Menus:Left:Menu--> and <!--System:Menus:Right:Menu-->

That last ":Menu" is an exclusion parameter, meaning "Don't show these menus, even if they would otherwise show here".

To remove the countdown timer, you'll need to just remove that relevant section from the HTML of the layout file.

Thanks Chops.