I have several sites build around the following model:

On the main domain :

I have a script running that does all kind of neat things (ebay, amazon , yahoo answers + a static front page )

I then have wordpress installed in mysite/blog

What I would like to do is Have only wordpress running for the site as a whole and remove the script on the main domain.

Not sure how to proceed and how to minimize ant SEO implications.

You can see an example of such site here:

New York Model Agencies

I appreciate any feedback

Regards,

Manuel