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As far as I know, a 301 redirect passes pagerank to the final destination, therefore if you get too many bad links it will affect your main domain rankings.
I would suggest you to create javascript tags that your affiliates can use to display banners, and links to your site and adding the nofollow attribute to those links created by the js.
There's a Matt Cutts video where he explains how 301 redirects work:
Nope, unfortunately, there's no way to export the pages that are linking to 404s.
If those links are valuable, you should set a 301 permanent redirect to the new page (where the original content used to be). By doing that the juice passes to the new page.
Here's the link that Fracisco refers to (I guess): http://www.seomoz.org/article/recommended
I've been using xml-sitemaps software for years now, their paid software is great. If you are running PHP based server, you just add the files to one directory and follow the installation steps. It will not only index the entire content, but you can also set limits on how many links per sitemap, they offer addons that automatically creates images/video sitemaps, news, etc. The software also creates an HTML version of the sitemap. And the XML version uses CSS so you can read it with ease.
I would go with them, the software even gives you info on how to submit the sitemaps to Google, sitemap index, etc. Then you can also create a link in the robots.txt so spiders know where to crawl:
Something like:
User-agent: * Sitemap: http://www.example.com/sitemap.xml
Oh, just spotted this video that refers to your question:
Sitemaps from xml-sitemaps are completely reliable. Google does not index all pages of your site and it also doesn't show the exact amount of indexed pages, that way the prevent users from using shady tactics to fool the system.
In my case, with about 4K pages submitted to Google via sitemap, about 3.5K are indexed (that's what it says in WT) but when performing a site:example.com search it shows about 5k results. So as you can see, those numbers that Google show are not exact, those are just estimates. If you submit 200 pages via the sitemap and google indexes only 10, then there's a problem.
As per your traffic change, you should look on another possible reasons, ans it could also take some time to reindex all your pages.
Basically, www domains are a subdomain of example.com. You don't need to have your subdomains like www.service.example.com, if that was what you were asking. That's just poorly structured URLs IMHO.
There shouldn't be any different for edu or gov domains.
I would definitely remove those links. They were unnaturally created. Although you are friends and you are not giving him anything in return (that you mentioned), do those links have any value for his visitors? I mean, when their users are on his site, are they likely to click on those links? If not, then not only those are useless backlinks for users but for SEO too.
As far as I know, the pin it button uses the image you give in the attribute. And if there's no image there, it will let you choose from all the images they find in the page.
There are a couple other scripts/enhancements you can do to speed up the site:
If the content gets indexed, then it's no longer protected for others to see. They could just search for the rest in Google.
There's no point of blocking users and allowing Google to index it. Instead, you could build pages with excepts of the content, so Google AND users can see that, then users can decide to proceed as a logged in user or not.
Google offers site authentication but only for AdSense purposes. You can give them the post details they will need to access that content, but that won't change the indexing for search.
Hope that helps!
Google indexes PDF contents and files almost like regular HTML. Links are followed, you can block indexing, etc. Just like regular HTML. The only thing Google can't index from PDFs are images, unless you have it in HTML format elsewhere.
I would definitely recommend converting those PDF menus to regular HTML.
You can find more info here:
Can google fully index pdf files?
Hope that helps!
Apparently there's a workaround for Canadian businesses:
http://www.stepforth.com/blog/2013/get-listed-on-bing-local-canada/
Hope that helps!
No problem! If you notice several bad backlinks, you could use a tool like removeem.com. Is a paid tool, but it will help you identifying those back links and contact the site owners. I hope you get it resolved.
There are several tools online to review your backlink profile. I would start with OpenSiteExplorer. Check all links and get those with very low authority, check those pages and see if they are related to your content, if there's no much value on them (content is unrelated, and the overall 'worthiness' is low) you could contact the webmaster asking to have that backlink removed.
I guess not, at least they shouldn't. But they were caught doing pretty ugly stuff 
They could still use your IP to personalize search, there's nothing wrong there.
Try using Cloudflare. They will give you lots of information about your traffic and block any bad traffic. You could test with their free service for a while, there's no need to pay anything. And once you have it figured out, you can go back to normal, or stay with cloudflare, which won't make you any bad.
Well, if you have cleaned your backlink profile, and there are still links that were not removed, you could try disavowing them using google's tool and see what happens. You should only use that tool if you are sure those are hurting you and have already done everything to contact the webmasters to have those removed.
If that doesn't work, then it is your content. Are you creating worthy content? Is people accessing your content pages? sharing it? Is that content really good for users? or was it built thinking on engines? Good, worthy content will give you some backlinks, which ultimately will increase your rankings.
If they are totally different services (that you need separate domains) I would go with different themes. Not because of a SEO penalty (there's none that I am aware of) but just because of user experience. Each Website offering a specific service would work better having the design matching the service, IMHO.
The only personalization Google can make if you are not logged in and have no cookies stored would be using your IP to trace your location. There's no need to keep track of your IP. Every request you make goes with your IP address, a simple IP tracing can reveal lots of information about you: http://tracethisip.com/myip