Help with theme and Javascript

Hi

I am fairly new to wordpress and I have a site I have built for a client using Pluck CMS the site is at http://www.saddlewerks.com

However I would like to move it to wordpress which I have a few problems with,

My wordpress site is at http://www.saddlewerks.com/wordpress/

1)How can I us a condition to stop it from putting the home page gallery in every page? the same as the original site.

2)The java is not working on the homepage, is there a conflict in the javascript? does anyone have any solutions?

Any help is much appreciated.