All very good questions there. If your planning on doing all that you just said, with the php and mysql, I would suggest (although frowned upon) using a package like WAMP or XAMP as they include apache, php5 and mysql 5 all wrap together. Just install and you have a working web server with php functions and the latest mysql.
The only catch is that, at least with WAMP, you will not have a root password installed by default for MySQL. The Emu requires this so you must make some changes using phpMyAdmin(included) then go back in and fix the phpMyadmin config files to allow it to connect using a password.
You then can proceed with setting up your emulator just like normal bypassing all the installation steps of mysql. Once you got it done, just open and forward all ports that your going to use, 5999,5998,7000-7100,80,8080 ect....
I can help more if need be just PM me. I would say do alot of homework first so you know what your really getting into, as it can be alot.
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