Is it possible to customise the login page for my customer portal? All I really needed to edit is the CSS for the page.
If thats not possible is there a way I can include JS into the page so I can manipulate the design via JS.
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You can do this by creating a Force.com Site and associating it with your portal. Then you can use VF pages for you portal. You can have a fully customized login page using any CSS or js you want. I would investigate using Sites
You can create your own login page and do what do you want on your custom login page.
Some links helps you to make things easy