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The only reason to get a different IP would be to host your site IN Canada. You don't have to do that, but it can help some.
Your ccTLD means that Google will recognize the sites are geotargeted. As Matt Cutts said, spammers really don't bother with ccTLDs (especially .ca, which is pretty restricted) so Google will generally figure out that duplicates are geotargeted.
I don't know that I would worry a lot about an RSS scraper, especially if they're using your brand as the link text. Most likely the site doing the scraping is already devalued.
What does the rest of your link profile look like? Is it mostly natural? I would assume that the Chicago Tribune (original content) would have lots of natural links.
If you were starting from scratch, I'd say do the subdirectory. But there's a cost associated with moving from an existing URL and the thing I preach is that, if you move, the reward needs to be better than the cost. In this case, I don't think you can say that. You can still move, but you'll lose some ranking short-term.
Do you see some long term gain I'm missing?
I wouldn't worry about one of your backlinks being infected. Google will probably flag their site but doesn't assume that sites it was linking to are bad.
One solitary link still can't really hurt you. Now if they have a sitewide to your site I might be concerned.
For bulk 301s you really want something like a .htaccess, that can globally instruct the web server where to send the traffic.
Incidentally, subdomains are now considered part of the root domain. Google said so. So you don't HAVE to move from your current structure if you don't want to.
I have a coworker who branded our reciprocal pages as "unethical" because we were "cheating" Google somehow.
That having been said...
The problem with this is that its a TON of work to run a link network. Even if we were all above board, what would the end value be? And what happens when Google's insert cute animal here update hits and knocks it all down? I honestly don't see any way for this to work in a long term because, as Mark noted, Google is trying to knock these sorts of things down.
I like how Amazon's CloudFront does this. It uses a CNAME to route it to the closest download site. I would do the same. Use something like Round Robin to split your downloads up. Or use a cloud based host to do it for you.
As far as SEO goes, it shouldn't matter. Google will do its own DNS and caching.
It depends. If the sites linking to you are strong in their own ranks you might not be hit. If they're weak, it seems a lot more likely that Penguin might devalue them or issue penalties.
It also depends on the links themselves. Are these sitewide links in, say, a sidebar or footer? I am beginning to think that Penguin might be seeing them as paid links but I can't say that for sure yet.
First off, I wouldn't panic. As the SEO Moz blog recommends, don't just start trying to take a hatchet to your links and assume that that will fix the problem.
Second, realize that a lot of what is going on with Penguin is algorithmic. That may not be any comfort, but I'm currently being beaten by generically popular sites, not competitors. There's nothing I can do until Google decides that they want to value quality sites again over popular ones. Did they penalize us for some backlinks? Possibly (when we started SEO years ago we did reciprocals with exact match keywords, one of the things Penguin is targeting), but the lack of highly relevant results (as in the pages getting #1 are simply popular sites with a page that mentions those words, not sites focused on them) for our primary terms means that Penguin, like Panda, penalizes first and fixes later.
Third, unfortunately, the only way to plug the hole caused by Penguin (we're down 15-20% in traffic on our #1 site over last year) is to buy Adwords. Get a budget and start a campaign. It's the only quick fix out there. If it is links sinking your ship, even nuking them all immediately wouldn't fix your drop and will probably hurt you more in the long run. Go back to SEO basics (quality content and building good links) and hope this storm passes soon.
As with many things in government, most of this is a "fix" to a problem that doesn't exist. If you don't want to be tracked, you can easily opt out. But the EU seems to think it knows better and declares that ALL cookies must be opt in only. This rule screams that it was written by people who want to push an ideology (i.e. government is going to save your privacy at all costs) and have no idea how the Internet works.
The largest problem with this rule is that there's no way to ascertain why a cookie was placed (most commonly called a session). In virtually all cases, cookies are pointers to something else. What's stupid is that you can still easily track people without cookies, you just pass your session ID in the URL. It's clunky but it works and there's no law against it. And there's always log parsing.
My bet is that there will be some sort of legal action taken against Google (the biggest fish in the pond) and we'll see where that goes. My bet is it stays in limbo until that trial is complete. I can't see anyone wasting the resources going after every violator.
We've been re-evaluating our titles and I think the real standard here is the same one content has always had: does it sound natural? In other words, would you ever say what you just wrote in a real conversation? Since you're repeating the words "Google Engage" and it's a bit runny on the grammar, I'd say it doesn't look good.
Why not say Google Engage Basic Training for Agencies?
Those are some sloppy URLs. I especially advise people to avoid the problems of relative paths in ANY URL. And, yes, <base> probably isn't helping.
Links starting with / are fine. That's the root of your site. Anything using "../" should be nixed and use a fixed path. And never, ever use "./".
What are Google Webmaster Tools telling you? Have you used it to tell Google your site is geotargeted?
In this case, no. Matt Cutts has stated that country TLDs that are duplicate are not generally seen as duplicate by Google.
I've noticed the same problem with the site. I wonder if it's related to the other issues SeoMoz has been having lately.
You might want to elaborate on why you have pages of duplicate content. I'm not sure I understand that point. Normally I'd say let your list be indexed and canonical the products. In fact, I'm not sure if a canonical on a list would help all that much.
Nofollow links don't pass PR. They are still spidered and ranked. A robots would work best to exclude an entire section of your website. And, yes, Webmaster tools will complain because you've cordoned off a large section of your site.
I seriously hope you have some unique content on your site somewhere because it sounds like you just de-indexed all your pages!
Per this page
You can only submit Sitemaps or URLs that belong to a website that you have verified through Google Webmaster Tools.
I agree with you. Keeping a second site with duplicate content makes no sense. Just 301 two.com to one.com (preserving URLs like two.com/widgets redirects to one.com/widgets) and you should have no problems.
Advertising has nothing to do with indexation. Google actively looks for domains (they are a registrar after all) and spiders them unless you explicitly tell them not to (i.e. robots.txt)