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I don't see anything wrong with your home-page canonical. We usually suggest pointing the home-page to the root:
...and not including the filename (just for the home-page), but that's not necessary. You link internally to "index.html", so what you have is fine, and keeps it consistent. I think the error is only happening because our crawler is trying to view the "/" version and sees the canonical to "index.html" (so, they look different).
So, just to be clear - these are the same physical page. Google sees the two URLs as being two different pages, but in terms of actual physical documents on your server, there's only one (ContactUs.html). So, you just need the one canonical tag per page.
If you have any dynamic (database/code-driven) pages, then be careful and make sure that the canonical tag is being create dynamically to match the correct page. You don't want to end up with canonical tags to the wrong pages.
I'd follow the advice to 301 or canonical, but it doesn't hurt to also declare a canonical version in Google Webmaster Tools - it's under "Site Configuration" > "Settings". You still need to canonicalize, but it's one additional signal to Google (and it's easy).
When you say "templates", can you explain what you mean? Do all 9 variations have the same content, but with a different wrapper (graphical look and feel)? In that case, I agree with @eyepaq - the canonical tag would be your best bet. It's a bit tough to tell with a specific example, but the key issue is how different the pages are (and if they have search value).
I have to disagree, though, regarding internal duplicate content not being a Panda issue. I think thin and near-duplicate internal content is very much part of the Panda equation. I've also seen large-scale duplication cause massive ranking problems.
Yeah, if it's essentially just a URL-shorterner, then that should be fine. It's how Bit.ly and other shorteners work - the 301-redirect passes the link "juice" to the appropriate page. I've built my own shorteners for a couple of sites and have never had trouble. For example, this URL:
...goes to...
http://www.usereffect.com/topic/25-point-website-usability-checklist
It's not being built on a 3rd-party platform (just home-brewed PHP).
When you're looking at 200+ ranking factor, there's a lot we can't account for even across all of our metrics. A few possibilities:
(1) The #2 site's links are being devalued, for some reason, due to quality issues.
(2) There are geo-targeting signals out of whack or focused outside of the US market. If the site is ranking #1 on Google.co.uk and has a clear UK connection, that could lower it's value on Google.com slightly. It's not the kiss of death, but it can make a difference.
(3) The #1 (currently on Google.com) site has recent activity that we're not aware of yet (link-building, especially).
(4) As Joshua said, #1 could be targeting inbound anchor text better.
(5) As Brandon said, #1 may have an advantage on user signals.
I don't think that Google currently "sandboxes" new sites in they way they may have once. What I think we're seeing is a grace period where new sites get a chance to rank while Google evaluates their link profile. If, after a couple of months, those links look spammy, the site may drop. In most cases I've seen, though, that's not a #1 vs. #2 sort of thing.
It's a trade-off, for both SEO and users, and I don't think there's one answer that fits every situation. The category level can add information, but it also makes URLs longer, which can be bad for both bots and people. If you have short, descriptive categories that aren't repeated in the product/page names, and those categories mimic your site structure, then I think it can be positive.
My argument was mostly against people adding categories just for SEO benefit (it's probably minimal, at best) or repeating every category, sub-category, etc. to the point of absurdity, causing keyword cannibalization and massive URLs. For example:
www.bobscamerashop.com/cameras/digital-cameras/canon-cameras/eos-cameras/camera-canon-eos-rebel-t3
Of course, that's also keyword stuffed, but I'm exaggerating to prove a point. You can go too far in either direction.
In general, though, I don't think categories in the URL are necessarily bad. In some cases, as Woj said, they could be a positive for users and possible even SEO.
I just want to publicly say that we're really trying to do a better job of endorsing answers in Public Q&A. The amount of activity since we relaunched Q&A has been beyond our wildest expectations (short-term, at least), and we really do appreciate the time our community members have spent answering each other's questions and sharing their experiences.
I really wanted to push the content marketing aspect in those slides, but I just want to add that it is a balancing act. Some manual link-building is fine - just make sure you mix in low-quality with high-quality AND make time to create solid content. In other words, just do everything simultaneously. As long as you don't need to eat or sleep, you'll be fine 
Seriously, carve out the content time, even if it's 20 minutes/day and it's the first thing you do in the morning. That investment will pay off. Waiting until you need content to create it is like only networking after you lose your job. It'll work, eventually, but you'll lose months.