[gizmo]

I could maybe help a little here Ash.
As for java, All my added JS I include in one file and call it js_all.tpl I put it in a folder, then use an include in home.tpl this way it calls it all up from there, so far works a treat, but this is only for my added JS for my tabs, accordions, and other mainly JQuerry js I have not tried us of yet to do what you are saying.

Give it a go on a test site and see how it works.

As to css, If you can get your head around sorting it all out (Maybe) I think the IE css fixes compatibilities would have to be kept different