I simply want to know how to do some simple custom tweaks to the code that is generated on a results of a search. The line and results of the search push out my web site layout and I would love to be able to eliminate that line or at the very least define it's width. I am using the cse in an iframe. Anyone know how to do this?

Which technology are you using? You probably have the greatest design freedom if you're using a server-side scripting language with the REST results from Google: http://blogoscoped.com/archive/2008-04-09-n26.html