PHP and MySQL natively run better on a Unix based platform since thats what they are designed for. I would personally recommend looking into acquiring Linux hosting for the job, not only is this cheaper but as long as you choose the right hosting company it can also be easier. Its often a case of upload and it works with maybe just a few tweaks of your directory paths since they're the most common thing to not carry over so well (I use the $_SERVER["DOCUMENT_ROOT"] global array variable when defining paths which solves these problems). Linux hosting machines are also much better streamlined to improve efficiency whereas windows server 2003 machines always come with the full contents of a desktop operating system (interface, graphical management tools etc).
Well I hope this will assist you when you make the decision. If you need any more advice on the subject (I've dealt with these things quite a lot) let me know and I'll see if I can help you out some more.
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