Yes you can select highlights depending on the clone by adding the clone class after the clone id. #highlight .clone_3
Example of where this is in firebug -
In regards to the spacing between the sections, you have numerous margins between the boxes, content, and postloop sections. Unfortunately we're unable to provide directly assistance with css changes as this is classed as site design, we're only able to provide you with links to the relevant resources to be able to learn how to track down the required resources to make the changes.
In firebug you'll see margins as yellow in the preview window, padding as dark blue. Scrolling through the html within the section you've selected in the inspector will help you to target these areas using the colors as a guide to where the css is applied. You can then edit/copy/paste back in to the framework to over rule the code.
For example -
So that would tell me to look inside the postloop area to see where further down the code to see where the margin is. So looking in there it was coming from the .article class. Then going further inside there, it there was more padding applied in the .hentry class. Going further .hentry-pad also had padding applied.
If you wanted to go further and remove the padding from above that area, you can reduce the #content .content-pad to bring the section up higher.