I have a website SNIP

The website allows the customer to upload affilliate banners, the affilliate code is normally a js file piece of code which the client adds to the website, the client cannot modify that piece of code as the .js file sits on the affiliate companies website.

The problem is that the .js file sometime contains .swf advertisements, on the website im implementing a hover over script which always seems to show below the flash file affilliate. I know the reason for this is the .js file wiith the affiliate code for a swf file does not have the wmode=transparent piece of code.

is it possible to modify the code in the js file on the fly and add the wmode=transparent piece of code? or is there a way to show the hover over feature on the website above the .swf affilliate?

please see picture of problem:

http://i33.tinypic.com/1zya72x.jpg