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A Magento store needs mod_rewrite enabled. Apache configuration might need some changes. The URLs are not working without index.php right now and they need to be SEO Friendly.
There is also a message on the admin side saying that the server is not configured properly. These two issues are probably related.
I don't have time to fix this myself. Need a quick fix from someone who knows what he is doing.
I will need details of what fixes you made after you're done.