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BTW, if they link to mysite.com/research/article7.html, will this help the rank of mysite.com ? What about a sibling or child page?
I think you need to go to them and ask them to link back to you. I would also ask them for a good yet short bio to be included. Nice if you can get it. The very least they should provide is a link with the keywords you want in the anchor text. Provide them with the code in copy/paste form, to make it even easier. Let them know you would be happy to provide them with more content if that would help, while pushing for the bio lines.
Linking to a directory page, off your main index page is fine and there is merit to that if you want to boost the link pop of internal pages. Let the site know you are happy to link to the page where your information is included.
To get them to put up links, I'd start with a nice request directed to the editor or other senior person (if you can find an individual). Just be polite. Offer to establish a link back, or point out that you already have.
If your remarks are taken from a copyrighted document, point that out, too. That might soften them up a bit.
Be polite, be persistent. Congrats on getting quoted - that's a great start! Good luck!
As far as the old links: Once the new site is up, I'd recommend contacting those sites linked to the old one with a request to alter the link to the new one. (This would be a good time to request any changes in the link text or site description.) In my experience, though, this effort will be only partially successful. Many smaller web sites are maintained sporadically or not at all. E-mail addresses change, or end up being ignored, too, so even contacting some of the linked sites may be problematic. With some effort, though, you should be able to get the majority of links shifted.
As rogerd says you should get some of your existing links changed but if I were you I'd start a new link building campaign.
It's not a bad idea altogether as you'll be able to look at this one fresh and any old links that you manage to get should be looked at as a bonus.
Sometimes it's better to start with a brand new site with no links as the strategy is easier to work out than trying to juggle between old and new. :)
Email all the webmasters of the links that you want to keep and then forget about it and start from scratch.