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The website: http://www.bouldertherapeutics.com/
Website hacked: End of June
Website cleaned and verified by sitelock within days
Number of indexed pages pages drop from in the 100's to just a few
Organic search visits dropped from 1600 in June to just over 400 in July
No messages in webmaster tools. No website changes. No link building done.
I have a client who had their WordPress site hacked. At that point there was no message from Google in webmaster tools and the search results for their pages still looked normal. They paid sitelock to fix the site. This was all about a month ago.
Logging into Webmaster Tools now there are still no messages from Google nor anything on the manual actions page. Their organic traffic is essentially gone. Looking at the submitted sitemap only 3 of their 121 submitted pages are indexed. Before this all of them where in the index. Looking at the index status report I can see that the number of indexed pages dropped completely off the map.
We are sure that the site is free of malware. This client has done no fishy SEO practices. What can be done?
Yes you can see this in two places:
Within Adwords you can go to the keywords tab and there will be a button directly above your list called "See search terms".
In analytics go to Traffic Sources >> Adwords >> Keywords. Then if you look at the drop down in the second column that currently has "none" selected you can chose "matched search query" and that will show you as well 
You could basically run two separate reports and join them together in one spreadsheet. One from Google's keyword tool (the competition is PPC based data but a good indicator) and the second from your SEOmoz account for rankings and get a similar view to what you have but much faster. The one thing you would be lacking is the target URL. Raven provides the adwords competition data next to its ranking view as well.
I believe they say you lose some link juice through a 301 redirect so ideally make the URL's the same. WordPress has a lot of easy to handle options with it's permalink structure to mimic most URL set ups. If your old URL's weren't very "seo friendly" then you should make better URL's on your new WP site and 301 the old to the new.
If your developer will be making the website dynamic via a system like WordPress there will be automated ways to keep your sitemap up to date every time you publish a new page to your system and then it will even ping the search engines that the sitemap is updated It will be a "set it and forget it" type of thing with sitemaps if you are moving in that direction
Good luck!
If you arent already, you should get either the SEO plugin by Yoast or the All in One SEO Pack for your WordPress install. Both of them will add fields on a per post and page level where you can enter your Meta information.
This is a really quality oriented service that helps to get your articles on other websites via guest blogging:
You should definitely bring your blog over to your own domain for all of the reasons you described already. Something like www.domainname.com/blog would be pretty ideal. This white board friday you should watch as well. It's really relevant to your question
http://www.seomoz.org/blog/mixing-viral-content-with-business-content-whiteboard-friday
It will find any page on your domain that is ranking for the keyword..I think the exception may be finding pages that rank across different sub domains (dont quote me on that though!)
For instance I have www.domainname.com set up under site definitions but the rank tracker is tracking my rank for pages like www.domainname.com/sub-page-that-ranks
You should definitely bring your blog over to your own domain for all of the reasons you described already. Something like www.domainname.com/blog would be pretty ideal. This white board friday you should watch as well. It's really relevant to your question
http://www.seomoz.org/blog/mixing-viral-content-with-business-content-whiteboard-friday
You will want the comments on the same page as the actual content for sure. The UGC on the main page will help keep it fresh as well as being another possible reason for people to link to it. Asking a user to browse to a second page would make it that less likely they would actually comment as well. Keeping it simple would be best. It's kind of the same idea as to why you would want to have your blog on the same sub domain as your main site as in the newest whiteboard Friday.
Yes you can see this in two places:
Within Adwords you can go to the keywords tab and there will be a button directly above your list called "See search terms".
In analytics go to Traffic Sources >> Adwords >> Keywords. Then if you look at the drop down in the second column that currently has "none" selected you can chose "matched search query" and that will show you as well
If you arent already, you should get either the SEO plugin by Yoast or the All in One SEO Pack for your WordPress install. Both of them will add fields on a per post and page level where you can enter your Meta information.
This is a really quality oriented service that helps to get your articles on other websites via guest blogging: