Welcome to the Q&A Forum

Hmm... not totally sure on why only half of your sitemap is being indexed. Likely its a mixture of a number of factors including (but not limited to) site age, NoIndex tags, Google not crawling deep enough, lack of inbound links to deep pages, etc. etc. From what I've seen though, Google will eventually get to all/most of the pages in your sitemap and will eventually swap out your older pages for the 301'd/canonicalized pages that you want showing in the SERPs. Take into account some of the other tips people are sharing here because it may be a mix of our suggestions that will ultimately work for you.

Okay, in that case I wouldn't suggest manually fetching and submitting 3000 links one by one because that would be a complete waste of time. You could always make sure to update your sitemap and then add that in Optimization>Sitemap or choose to Resubmit the current sitemap (hoping that that will lead to Google re-crawling sooner) and/or fetch some changed pages and submit to index as "URL and all linked pages".

Otherwise I'd say wait... SEO is a long-term job. It's only been 6 weeks since you re-did your site and less than that since you switched everything over from 302s to 301s. Give it some more time and you'll see Google start showing the correct pages and removing any unnecessary duplicate content warnings.

As far as I know, there is no problem with doing that. Hell, look at the page titles for everything here in the Q&A forum... they all end in " | SEOmoz Q&A" and the pro pages all seem to end in " | SEOmoz PRO".

The sites I work on all do that with their blog pages. Every page gets an individual title but they all end with the stovepipe and the blog's name. It definitely cuts down on the effective space to work with for optimizing your titles but it also potentially adds in a branding signal that could help your site overall in the long run. We've never had any duplicate title warnings associated directly with that repetition.

Edit: Here's something straight from SEOmoz's Title Tag Best Practices page http://www.seomoz.org/learn-seo/title-tag

It even lists the optimal format as Primary Keyword - Secondary Keyword | Brand Name or Brand Name | Primary Keyword and Secondary Keyword

Sometimes it can take a while for Google to show things correctly in the SERPs and for a time you may wind up with duplication warnings because there is the older, cached page still showing in the index along with the new page that the older one redirects to. In cases like this I usually jump into webmaster tools, fetch the old page (which I know redirects to the new one) and do a crawl request/submit to index to ensure that Google sees it and indexes it correctly sooner than it may have naturally. Now, I'm not 100% certain that it will fix your issue but I can say that it can potentially help and can't do any harm in this instance.

I more or less agree with EGOL. Directory Submissions are a thing of the past and are likely to get you in trouble nowadays. Getting backlinks is becoming harder and harder everyday. You need to diversify more and make sure that all those links to you look as natural as possible. It's not a bad thing to do linking yourself to get that initial push but the best possible linking strategy is a naturally occurring one. Make sure you use all relevant social avenues open to you... Facebook pages, G+, LinkedIn, Pinterest, Instagram, StumbleUpon, and so on as long as it make sense for your site to be there and you keep up with posting. Hopefully those will generate natural links back to your site as people learn who you are and grow to like your site.

Her general example was based on her, Matt Cutts and another Google employee having Fitness websites that she then buys and how she would go about the use of canonicals and 301s to show users and search engines that she is the most relevant authority. One of the pluses with the canonicals involved branded searches that would still pull the Matt Cutts site instead of the Maile Ohye site but link equity would be directed to her site and users would be less likely to bounce since the canonical would serve the Matt page whereas a 301 may be jarring at first because if you're looking for Matt and get Maile you may be more likely to bounce even though its the content you are looking for.

(God, I swear I can explain this better in my own head than I can once I attempt to write it out... which is bad considering I actually make a living writing)

Similar page titles aren't the end of the world but its always good to diversify. If you have Google Analytics set up for your site, maybe you could take a look at what terms those other pages could be ranking well for where you aren't already page one and then try optimizing for those terms. When Google made those changes to domain diversity in the SERPs it made it a bit harder to appear two or more times on the same page 1 but that doesn't mean you can't try to appear on more page 1s instead.

This reminded me of something Maile Ohye from Google was talking about at SMX NY.

In her talk about 301 vs Rel=Canonical she brought up the idea of putting notices on a site first that Site A is now a part of the Site B Family and will be consolidated in the future and giving people (and the spiders) a link to the new site to start building relevancy. Then later on implementing canonicals across Site A pointing to the relevant places on Site B. Gradually moving towards 301 redirects once Site B becomes the place people now recognize as the main site and the original is no longer needed.

[This of course is all paraphrased and from memory as I don't have my voice recordings of the session handy nor did anyone from Google provide PDFs of their slideshows]

Have you checked for instances where a page parameter is being seen as another version of the same page? One of the sites I work for had an issue a few months back where every instance of a product page was being flagged as duplicate content because of an oversight. We had one of our coders write a clause into the page where every time a page loaded with a parameter such as ?color=72 it would canonicalize it to the page minus the parameter. This decreased our duplicate content warnings quickly and effectively.

Crawled and indexed is the easy part: Google Webmaster Tools and/or Bing Webmaster Tools, Submit a sitemap, do a crawl request of the page once it goes live, try some easy social bookmarking like StumbleUpon. That should be a good start at least.

Now ranking well... that's the hard (fun) part.