There shouldn't be any files you extract there until you install the database. And even then, there should be only one folder aside from the MySQL files from the installation. I honestly couldn't tell you what you did wrong. I installed it according to that guide and didn't have any issues what so ever.
You might want to uninstall everything, delete the residue folders and make sure you follow that guide word for word. If you're having issues with the dos window closing, then I'm almost certain you didn't install MySQL correctly.
By funny chance, I hope you're not typing "C:\mysql\bin\mysql -u root peq" with the quotes. :P
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