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Hi there, This is currently being addressed in the support ticket you created so we'll continue the conversation there. Thanks!

Yes and No, i dont think that these redirects are directly harming your seo but having a home page on the base url does help in terms of allowing visitors to feel comfortable. I think the main issue that could harm your seo is that perhaps that you or someone else in the past or future has built links pointing to your home page which does not exist. If you are going tyo keep it as is then the priority needs to be on this extension of your domain and flow out to the rest of the site. Hope this makes sense.

It can actually take up to sixty days (two crawls) for the links to show up, if you happened to have built links right as one of the crawls was finishing. Unlike Google, Linkscape (in the past) crawls about once a month -- spends a couple of weeks crawling then a couple of weeks processing. Your links should have shown up by now for sure, let us know if they haven't for some reason.

Is your site verified in Google? Try logging into Google Webmaster Tools and looking at the 404 report there. It often will list the incoming link for a 404 error.

Thanks Alan.  That's really helpful and not something I was aware of.

This may make it a little easier to carry out. http://www.htaccessredirect.net/ A 301 redirect to the root domain should do the trick.

I would always carry out analysis of the site I was working on before I look at competitor analysis.Keyword analysis would form part of this to ensure that I knew what relevant words and phrases should be targeted. Next I would look at the content of the site to see if it contains the phrases in all the relevant places (title tag, alt text etc). A key task would then be to make sure there are no technical issues reducing the chances of your site ranking highly. I would look to get the on-page elements sorted before focusing on link building as the site may not deserve a link until on-page issues are sorted out. With regards to the benefits of article submissions and social networking I would advise you to research these areas a little more as low quality articles strewn across the web may not be the best course of action and social media aspects may or may not be worth chasing depending on whether there will be ongoing resource available to support the initial efforts.

SEOmoz has also recently revamped their list of directories. You might check out the post about link building via directories (with a link to the list) at http://www.seomoz.org/blog/seo-link-directory-best-practices.