Not an answer to your problem but your insight will help on a related issue.
Does the website run ok with app/code/core/Mage/Install/etc/config.xml reverted back to the original with the rest of SUPEE-5994 installed?
I'm asking because some people are having issues with 3rd party modules causing 404 status errors in the admin backend due to the fact that said modules weren't properly programmed to have proper security.
The correct answer is "Contact your module developer for a patch so we can run the patch", but expediency says "do what you can to keep the website up until you get the patch for the patch". Alas, what a cruel world, sigh, sigh, groan!