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First, I'd say that just because Moz does not flag a page as duplicate content does not mean Google would not think it is duplicate content. As great as Moz is, even Moz cannot know for sure what Google thinks about any specific issue.

Second, I'd look at your keyword research. Are people searching only for general, category-based terms such as "Acme Pond Pumps"? If so, then you might want to no-index all the specific product pages (that may have duplicate content). But if people are searching on a detailed, specific terms such as "Acme Pond Pump 100" and "Acme Pond Pump 200," then you want all of them to be indexed individually. In the second example, I'd try to make each product page as original as possible -- which is something you seem to be doing.

I wouldn't worry about passing "link juice" upwards. As long as you have a flat hierarchy so that all of the product pages are no more than three levels/clicks away from the home page, there should be no crawling/indexation issues.

I hope that helps -- let me know in a reply if you have any other questions!

Whenever I ask myself if I want to pursue a such a specific link actively (paid or unpaid), I ask myself three questions:

1. Would I want this link if Google did not exist? (i.e., would the link send me valuable referred traffic anyway?)

2. Is this link curated by a human who is an expert in the field and who does not accept each and every submission?

3. If this link is being paid for, does it not pass PageRank (i.e., is it a no-follow link that adheres to Google's guidelines as such)?

If the answer is "yes" to all three questions, the link is usually safe.

Now, your situation is interesting. The American Marketing Association is a recognized, authoritative resource. But if they are accepting paid listings, then I see in the source code that they are not no-following the links -- which directly goes against Google's guidelines. So, I would play it safe and not buy a listing there. Plus, the fact that they put the paid directory on a subdomain makes me uneasy -- it seems like they did that as a safeguard so that if Google would ever penalize the subdomain, it would not affect the site as a whole. I'd also think that they'd know to no-follow paid links.

Instead, I'd see if you can somehow "earn" a link from that site at the root-domain level instead via content and PR and such.

The best way to get quality links is not to pursue active linkbuilding at all. The best way to promote your website (and business) and thereby "earn" links indirectly is the same today as it was decades ago: public relations to get coverage.

I'd suggest reading my Moz post on what I've called the "PR-based SEO process": http://moz.com/blog/an-introduction-to-pr-strategy-for-seos

First question: What can your company do that is newsworthy?

Based on the manual action message from Google, I would guess that one of the possible reasons is that the unindexed pages have bad links pointing towards them. So Google is thinking that those pages are not "quality."

I would also check that all pages are included in your XML sitemap at a minimum and HTML sitemap (if you have the latter one). I'd also check the section of all pages to make sure that no pages are set to "noindex." Lastly, you may have duplicate content. If two pages have the exact-same text with only minor keyword-based variations, for example, then Google will often index only one of the two pages.

First, I'd forget about doing guest blogging for the sole purpose of gaining links. Matt Cutts, Google's head of web spam, told us in clear terms that online marketers should stop doing this. (I'd add that people should not have been doing this in the first place.)

Rather, I'd focus on contributing to online publications for the purpose of increasing awareness and coverage of your company, website, product, and/or service among a specific, targeted audience. Don't worry about the links. They'll come naturally themselves as long as you do online PR in the right way.

For more, I'd suggest looking at my Moz post on the topic: http://moz.com/blog/an-introduction-to-pr-strategy-for-seos

In short, I'd focus on the websites from whom you would want links even if Google did not exist. If you sell widgets, then you want a mention -- with or without a link! -- on a website that is read by people who are interested in widgets. Think about this issue like this and don't worry too much about getting links directly.

First, I'd forget about doing guest blogging for the sole purpose of gaining links. Matt Cutts, Google's head of web spam, told us in clear terms that online marketers should stop doing this. (I'd add that people should not have been doing this in the first place.)

Rather, I'd focus on contributing to online publications for the purpose of increasing awareness and coverage of your company, website, product, and/or service among a specific, targeted audience. Don't worry about the links. They'll come naturally themselves as long as you do online PR in the right way.

For more, I'd suggest looking at my Moz post on the topic: http://moz.com/blog/an-introduction-to-pr-strategy-for-seos

In short, I'd focus on the websites from whom you would want links even if Google did not exist. If you sell widgets, then you want a mention -- with or without a link! -- on a website that is read by people who are interested in widgets. Think about this issue like this and don't worry too much about getting links directly.

I presume that your site is structured something like this way?

www.example.com/city1
www.example.com/city2

If so, then you must avoid duplicate-content issues and make each page as unique (and useful!) as possible. For example, each location-specific page could include a Google Maps snippet, a local address and directions, the local weather, the local phone number and local news, and so on. Companies that have offices in various cities can write about what specifically is done at each location -- for example, marketing might be in London, sales might be in Paris, and so on. Perhaps include photos of the people at each office. List local prices (if relevant). Be as creative as possible. Obtain links to a specific location page from authoritative sites in and about that locality. In your banner or footer (or elsewhere), use anchor text like "London" and "Paris" for the links that take people to the pages with information about the "London" and "Paris" offices.

Does that help?

Having the same products in different categories is not generally a bad thing as long as you create canonical versions. I'd read this Moz post that may greatly help you: http://moz.com/ugc/ecommerce-seo-creating-collections-based-on-searches

Depending on the number of keyword targets, you may want to do one of the following:

1. Create category pages in the style of "collection pages" as described in the post
2. Create the collection pages as a layer between category and product pages

Then, customize the category/collection pages as described for maximum SEO benefit.

Lastly, choose one specific product page in one specific category and make it "canonical." Then, use the rel=canonical tag on all of the pages for that product in other categories so that the tag will point to the canonical version. You should be good to go!

I presume that your site is something like this?

www.example.com/london
www.example.com/paris
www.example.com/new-york

If so, then you are correct to avoid duplicate-content issues and make each page as unique (and useful!) as possible. For example, each page could include a Google Maps address and directions, the local weather, and local news. Companies that have offices in various cities can write about what specifically is done at each location -- for example, marketing might be in London, sales might be in Paris, and so on. Perhaps include photos of the people at each office. List local prices. Be as creative as possible.

As far as categories, I presume you are asking whether to do this:

www.example.com/category-1/london
www.example.com/category-1/paris

or this:

www.example.com/london/category-1
www.example.com/london/category-2

To be honest, there is no set answer. It depends on the keyword research, the content, the vertical and industry, and many other factors. Can you clarify your question?

It's impossible to get past rankings. You can only start to monitor them now and then record the changes manually or with a program. One example is Moz's Rank Checker (subscription required): https://moz.com/researchtools/rank-tracker

However, rank is increasingly a useless term because every person in the world sees different SERPs pages based on his or her location, language, search history, Google+ use, and a lot more. The closest that you can get is to get non-personalized rankings for a given location, but even then, that will just be an estimate.

The only directories that I would pursue are relevant, human-run, curated lists. Ignore those junk directories that accept every submission (paid or not).

Think about it like this. Say I'm a local restaurant. I find a local food reviewer and blogger who publishes a list of his favorite restaurants in my city. I would naturally want to be included in his list because it is authoritative and valuable. I would not want to be included in a junk directory that contains every site in my city.

The more selective that a list or directory is, the more authority that Google is likely to ascribe to it.

First, I'd forget about doing guest blogging for the sole purpose of gaining links. Matt Cutts, Google's head of web spam, told us in clear terms that online marketers should stop doing this. (I'd add that people should not have been doing this in the first place.)

Rather, I'd focus on contributing to online publications for the purpose of increasing awareness and coverage of your company, website, product, and/or service among a specific, targeted audience. Don't worry about the links. They'll come naturally themselves as long as you do online PR in the right way.

For more, I'd suggest looking at my Moz post on the topic: http://moz.com/blog/an-introduction-to-pr-strategy-for-seos

In short, I'd focus on the websites from whom you would want links even if Google did not exist.