I agree, lose the popup.
The other thing I’m assuming the menu is in dhtml
I’d be looking at including a sitemap and pointing to it from your footer of the home page.
Like yourself, I’ve got way too many pages to just add these to my footer. The site map provides a good easy to crawl resources for SE’s. Try to keep it as sparse as possible and don’t make the mistake some by plastering promotional media all over it either. Plain and simple is the key imo to a good sitemap.
The other thing, instead of running some style’s on page (
Doing that is going to cut down the amount of code you have. I’d also consider using your own tracking resource too. extremetracking is one of the first off site URL’s that a SE spider will find on your site. IMO your only encouraging it to leave your site, by placing it there.
Apart from that I like the visual flow and eye catching design.
Cheers