Thanks guys for your feedback.
I thought of your method @PicnicTutorials; which would do what I want. The only issue is there would still be white spacing in the file.
It's for a fully featured theme so it would make sense to include them on all the pages. Currently they are included on all the pages. Thanks for the link, this would prove useful in this theme. Not sure if you can have this on the WordPress installation. My original intention is to have a single CSS and a single JS file which would run all the scripts on the website. I feel if I was to run assestic it would automatically give me the minify version of each.
The only trouble is some scripts are needed before the header and other before the body, so I would be a little puzzled on wether two files would be needed to make sure everything runs as it shou;d.