Re: Alignment is OK in my frame, but not as new window?
Bigger problem - Have you tested any payment methods? Most methods that have to communicate with your site will not work with the Zen Cart shop in a frame. You have a very simple clean look and would be much better off styling your shop to match the rest of your site.
Please do not PM for support issues: a private solution doesn't benefit the community.
Be careful with unsolicited advice via email or PM - Make sure the person you are talking to is a reliable source.