The zip file "cm-9.0.0-crespo4g.zip" is still on my Nexus S taking up room (as is the gapps zip), can I remove it or will that cause an issue?
Yes after you have flashed both. I however keep them in a folder on there because I often times forget what version of something I am running and if for some reason you would have to reflash. But to answer your question specifically yes you can delete them