wheel - 3:17 pm on Sep 7, 2011 (gmt 0)
Don't worry about run of site links. Any site that gives you a footer link that has 5000 pages will show that number of links - it doesn't mean anything on it's own.
Many of my inbound links are run of site, they come from blogroll links on popular blogs - so I have a link from every page of those sites. It's no big deal.