I think you are over-egging your omelette...

Before you start really hacking away at the code, just make sure that needed php files are in their respective directories.

You say you have an over-ride for footer.php that is not working?

Then either REPLACE it with the original core, or do a COMPARE (using winmerge) to see where possible problems may lie.

As this is your first post, and you have just joined, I assume your store is not trading. So it's safe to revert.