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If you're not proficient in programming, you might consider finding someone who is, and having them look for you. The size of the site/script would determine what someone like that might charge, as well as their general experience level.
Sometimes, backdoors hide in unlikely places, like the user permissions in MySQL. You have to look under a lot of rocks.
In my experience, backdoors, etc, are generally pretty rare, and are often only inserted by Freelancer / Rent-a-Coder types.
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