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Matt Cutts says not to use nofollow on internal links. He says that causes pagerank to evaporate and that Google has made changes so that pagerank sculpting doesn't really work. He is pretty definite about this.

http://www.youtube.com/watch?v=4SAPUx4Beh8

http://www.youtube.com/watch?v=bVOOB_Q0MZY

Rand did a good Whiteboard Friday about this earlier this year.

An excerpt from the talk:

So let's say you've got blog.yoursite.com or you've got www.yoursite.com/blog. Now engines may indeed consider content that's on this separate subdomain to be the same as the content that's on here, and so all of the links, all of the user and usage data signals, all of the ranking signals as an entirety that point here may benefit this site as well as benefiting this subdomain. The keyword there is "may."

Another:

Bottom line is it's really dangerous to put content on a subdomain still. I believe John and I believe Matt when they say that Google has made strides in this direction. The problem is they're not good enough or perfect enough to rely on that factor, and so I'd really urge everyone to keep your content on one single sub and root domain, preferably in subfolders. That's how you're going to maximize your potential SEO benefit. This is one of those technical SEO things that just hasn't changed for many years now.

You cannot change it. Google does not allow Moz and other sites to use their data this way, so that is why Moz uses Bing. To get Google data, you need to sign up for Google Adwords and use their tool. (You do not have to be actively using Adwords, just signed up.)

The best way to fix this is with a rel=canonical URL. Tag each page with the lower-case version. (I had this same problem.)

SEMRush will do this. In their interface under Organic Research is Positions, which shows which keywords you rank in the top 20 for organically. Unfortunately it is a paid tool, but for free you can see how many keywords you rank for and what the first ten are.

Noodp= No Open Directory Project
Noydir= No Yahoo Directory

These are used if your website is listed in one of these directories with information you do not want used in the results pages. This might be the case if you have old, outdated listings that no longer apply. They tell robots not to use information from these sources, and they are optional.

It is not unusual for the same page to be reachable by multiple URLs. This can be caused by tracking parameters or site search results (which is what I think is happening in your case). The easiest fix for this is putting a canonical URL on the page using the one Google has indexed. But keep in mind that duplicate content does not cause a penalty as such, it just causes Google to make a choice about which URL to display in the search results and it seems that choice has already been made in your case. (I would still add the canonicals, though.)

In theory, a nofollow link should not transfer authority. However, I recently read an article by Christopher Cemper of LinkResearchTools that kind of argues otherwise. (He mainly talks about nofollow links passing negative signals.) I don't think it is possible to assign a number to this—it's one of those things Google likes to keep to itself.

In any case, relevant links from high-quality sites are a good thing, whether they are nofollow or not.

I will be attending. (My first time.) I am looking forward to it!

Here is a good Moz article on the subject: http://moz.com/learn/seo/anchor-text . It includes examples.

"Key Points:

• If many links point to a page with the right keywords in their anchor text, that page has a very good chance of ranking well. Real examples of this include the search engine result pages for the queries, "click here" and "leave." Many of the Google results for these queries rank solely due to the anchor text of inbound links.
• People have a tendency to link to content using the anchor text of either the domain name or the title of the page. This is an advantage to SEOs who include keywords they want to rank for in these two elements.
• Too many inbound links to a page with the exact same keyword-rich anchor text may cause Google to scrutinize that site’s link profile more closely; using manipulative methods to acquire keyword–rich anchor text is not recommended."

[The emphasis is mine.]

And for outbound links: http://moz.com/learn/seo/external-link

"Optimal Format

Use descriptive keywords in anchor text that reflect the same topic or keywords the target page is trying to target. It's not necessary to use the same keyword text every time—in fact, doing so can trigger spam detectors. Instead, strive for a variety of anchor text that enhances context and usability for your users—and for search engines, as well."

Here is a nice article on the subject: http://www.searchenginejournal.com/google-recommends-using-xml-sitemaps-rssatom-feeds-optimal-crawling/118364/

"Google explains the differences between the formats by saying that XML sitemaps describe a whole set of URLs within a site, while RSS/Atom feeds only describe the most recent changes. As a result of XML sitemaps containing more information, they are typically larger than RSS/Atom feeds. XML sitemaps are also downloaded less frequently.

As a website owner, which format should you use if you want your website to be crawled to the best of Google’s ability. Google recommends using both, explaining how the formats compliment each other."

A good idea is to keep track of a couple of your competitors' domain rankings, so you can see how you are doing relative to them.

Another quote from the link that keszi provided:
"It's best to use Page Authority (PA) and Domain Authority (DA) as comparative metrics when doing research in the search results and determining which sites/pages may have more powerful/important link profiles than others."

So if you see that your site went down and your competitors' went down as well, you'll know not to be too concerned.

Looking at your code, I see:

name="robots" content="noindex,follow,noodp,noarchive,noydir" />

That page appears to be noindexed. Check your settings.

If you have Yoast (SEO Plugin) you can do that in the settings. (Choose Titles & Metas, then click on the Taxonomies tab.) You can also do it directly, under posts > categories.

You could have your affiliates do a cross-domain canonical, pointing to the original content on your site.

Why do you have the magazine on a separate site? You could instead make a subfolder on your current site, like this: http://www.gulfstream.com/nonstop-magazine . That way all of the lovely links you get will help boost both of them.

When you 301 redirect www.site.com to site.com, as long as the redirect is in place, the "link juice" will be passed from www.site.com to site.com. [And as the saying goes, there are no stupid questions...]

Where does your client fall in the chain of command of the company? If s/he is at the very top, sunk costs should not dictate keeping a bad website, and if something different is better for this one product then it is better for all of the products.

But assuming they can't have a total site redo, why not use a subfolder? Although Google's John Muller said subdomain or subfolder does not make a difference, there is enough evidence to the contrary that I'd go with a subfolder if at all possible.

Perhaps the subdomain is because the person wants to distance this part from the rest of the site.

But as we know, a big part of SEO is the way things are linked (including internally) and one robust, well-linked site is stronger than a string of independent microsites, which is partly why microsites are not popular anymore. And existing links to the overall domain will help boost this new section if it is correctly integrated. (Unless the rest of the site is really terrible, in which case this one section probably won't make much difference either way.)

I don't think subdomain/subfolder is the main issue here though. It seems that your client want this product separated--does that make the most sense for the overall business goals of the company (as opposed to the success of this one project)? That's the question that needs answering.

Way back in 2012 Matt Cutts said:

“I read a post by someone offering new top-level domain (TLDs). They made this claim: ‘Will a new TLD web address automatically be favoured by Google over a .com equivalent? Quite simply, yes it will.’

“Sorry, but that's just not true, and as an engineer in the search quality team at Google, I feel the need to debunk this misconception. Google has a lot of experience in returning relevant web pages, regardless of the top-level domain (TLD). Google will attempt to rank new TLDs appropriately, but I don't expect a new TLD to get any kind of initial preference over .com, and I wouldn't bet on that happening in the long-term either. If you want to register an entirely new TLD for other reasons, that's your choice, but you shouldn't register a TLD in the mistaken belief that you'll get some sort of boost in search engine rankings.”

and I have not seen anything to indicate that this is no longer true.

Some people like to get the new tlds because they feel that they will be attractive to the user, that if for instance people see a .tv they would choose it over another page because they would think that a .tv provides a better video experience.

This may be true, but on the other hand, there are plenty of people who no longer think of tv when they think of the video experience...

You should write your description in a way that will make people want to click on your link when they see your description in the search results.

But be aware that Google won't necessarily pick your description to show—it shows what it thinks best matches what the searcher is looking for. If your description is heavy on keywords that are not on the page and does not contain words that reflect the content of the page, it probably won't get shown.