It looks like there's been a pretty quick update to this thread. A new member Tony (travelsignposts) has posted a response related to the issues I've addressed above. Apparently a developer has created a Wordpress plugin called
W3 Total Cache which will combine .js and CSS files. Not too bad.
There still may be one problem though, that being, that this solution requires a plugin and is not actually within the chore Wordpress files so updating the plugin could cause problems - I stress could but that possible 1% chance renders my site one percent less optimal than I'd like it to be.