I'm approaching this from a user performance and usability point of view. Which would make the pages load the fastest and be usable by the user faster?
A. Having a single Javascript file linked from the header that's 10kb in size that includes variable definitions and several functions, one of which being a $(function() that, if I understand correctly, loads as soon as the document is complete;
B. Putting the variable definitions in one file that's linked from the header that's roughly 1kb, then a second Javascript file for the functions that's linked from the footer that's about 9kb... causing 2 connections, but the larger one being called at the end of the page;
C. Putting the variable definitions directly in the header, adding 1kb to the size of the header file and removing the ability to cache the Javascript variables, but also removing one of the HTTP connections... and then putting the functions in a separate 9kb file that's linked from the footer, like in option B; or
D. Something else altogether.
Then on a similar note:
1. Having a single CSS file linked from the header that's 25kb in size and holds CSS for the entire website;
2. Having a smaller CSS file linked from the header of the homepage that's 8kb in size and only holds CSS for the homepage, then a second CSS file linked from the footer of the homepage that's 17kb and holds CSS for the rest of the site (assuming that putting it at the bottom would let it be cached for the rest of the site); or
3. Something else altogether.