Ideally one version of the site should redirect to the other version using a 301 to transfer any link juice from one version of the domain to the other.  In an issue where both versions have links pointing to them, the best solution is to see which version has the highest domain authority and the most links and use that as your preferred domain.

A lot of SEO clients we have are real estate agencies.  We always recommend that you diversify this information so as not to canibalize your own keywords.  We generally suggest location (such as Edmonton) and then other top keywords for your area, usually stuff like

Edmonton Real Estate

Edmonton Homes for Sale

Edmonton Property Listings

etc.

We also suggest that you really take advantage of specific location searches, so if you have a property listing page in a specific area, it is a good idea to include the zip code.  This is where keyword data provided usually fails and you need an intimate knowledge of your area/industry because people often perform searches based on yard signs they have seen - and there will be no keyword data for this.

I haven't used any of these services or tools, but I took a look at what you listed.

Removeem is more of a link management tool that lets you note who you've contacted and what the status is.  That seems really useful if you don't want to keep track of all this another way, such as Excel.

I am personally a bit hesitant to use "link removal services" but that's just me.

I also haven't had a chance to watch this yet - bookmarked it for when I have time.  It is a webinar from SEOGadget about link removal.  SEOGadget really knows their stuff so I am sure you will find some valuable advice in here.

https://seogadget.co.uk/adventures-in-link-removal-slides-and-webinar-recording/

They are aware of the issue.  Their twitter stream https://twitter.com/SEOmoz has a tweet from 8/31 about the issue:

"Uh oh. It looks like our Keyword Difficulty Tool is having some.... difficulty. We're working on it now. Stay tuned, friends."

So they are working on it!  It is labor day weekend so it may take em a little extra time to get it up and going.

In the meantime, if you are in dire need of KW difficulty, you can get some basic insight the following ways:

Use Google Keyword Tool and look at the "Competition" level.  While this area refers to competition within Adwords - this can also give you a basic idea of how competitive the keyword is overall.  If it's a highly competitive Adwords term, chances are likely that SEOs are after it organically as well.

Do a quick check of the organic SERPs and check out the domains in the top placements or even on the entire first page.  Are these really high authority domains, how well optimized are they, etc.

I think with that you would risk the chance of Google viewing those as paid links, so I would be careful.  I think you should request that some of them be no-followed.  Then work on attaining other types of backlinks with that strategy, through stuff like guest posting and writing quality articles on your own blog, doing some type of interesting study in your niche that may be posted to news outlets, etc.

Well, everyone might define "quality" different - so I would hate to say "yea that's TOTALLY fiine" but then find out that quality backlinks meant 300 press releases to you

What are you going to be doing to earn the backlinks?

Affiliate sites are hard to rank because a great number of them are thin pages, scraped content and basically provide little value.

Affiliate sites in the pills, porn or casino niches will also be a lot more difficult to rank... but if you are opening up an affiliate site outside of those niches, and concentrating on providing useful content, then it should be just as difficult as any other site - depending on the competitive landscape.

For paginated pages, I recommend using the rel=next and rel=prev tags.  Here is more info:

http://googlewebmastercentral.blogspot.com/2012/03/video-about-pagination-with-relnext-and.html