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For the server I would recommend WAMP or XAMPP. As for editing the PHP files my favorite editor is PHP Designer because it has a built in debugger, but it costs money. If you are short on cash I would recommend using Notepad++ to edit the code.

I would recommend checking out Tiztag and PHP.net to learn PHP. Those are the two sites I learned PHP from.

I think it looks really cool. I already saw a port of QUAKE for it that Google did.

It will not affect your ranking unless you changed pages completely or moved where they are located.

What web browser are you using to preview the flash in? Also, could you provide a sample of the code you are using to embed the flash with?

It looks really nice for a first site. But I would recommend trying out some gradients to add a little more "flare" to the design.