Thanks Alan, you are right this site has quite a long way to go. The first crawl was just finished and I notice that the most errors were due to dupe content so I decided I would try and tackle that first. Thank you for all the pointers, I will be taking a look at all those as soon as I can.

When the crawl diagnostics came back for my site its showing around 3,000 pages of duplicate content. Almost all of them are of the catalog search results page. I also did a site search on Google and they have most of the results pages in their index too. I think I should just disallow the bots in the /catalogsearch/ sub folder, but I'm not sure if this will have any negative effect?

I would at least nofollow all the links, 100 external links is getting up there. In the crawl diagnostics on SEOmoz if a page has over 100 links it gets a warning letting you know that there are too many links on the page.