When the cart appears as an overlay inside your page like that, it inherits the CSS from your site/page, so your fruitstoroots site apparently has some CSS that applies to HTML elements in the cart. It would be up to you to tweak your site's CSS so that it doesn't apply to cart elements anymore.
You may find the View Source Chart extension for Firefox helpful to examine the HTML structure of the cart and figure out how your CSS selectors apply to that:
https://addons.mozilla.org/en-US/firefox/addon/655/
Once you have that extension installed, you can view the cart on any page and, while the cart is still visible, right-click on it and select View Source Chart. You will find the cart structure added in its own DIV at the end of your regular page source. That DIV has id="EJEJC_window", so you might take the approach of just adding some declarations to your site's CSS making special exceptions for anything nested inside that ID.
The "Special Instructions" text is coming from these cart customization lines; you can remove them from every page to remove that text:
function EJEJC_config() { EJEJC_POSTCALL=true; }
function EJEJC_shown() {
jQuery('#tdSell').attr("innerHTML", '<div><blockquote>Special Instructions: </blockquote></div>');