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My site has been out or at the very bottom since last year, the home page only came back a little for main kw a couple months ago with PR1, after the update started last month my home page was back for main kw on page one and ranged between #2-#4 with the PR increased from 1 to 2 but still no internal pages or back links. This month's update the PR increased from 2 to 3, but still no back links or internals - until this morning when I found a number of internal pages listed on page one.
Still, there are no back links or related pages from the tool bar or by using the link:mysite.com mysite.com command. However, using links: mysite.com (with a space after : ) it shows 160 sites that do link to me. Most of them are not particularily high PR sites, and most of the PR4+ sites that do link to me are not in this list.
I'm not sure now what the cause for these pages being listed is because I've made several home page and sitemap changes since this update started. This could be the everflux instead of part of the update but I wouldn't have thought so many internal pages would get back in now just because of the everflux. The listed pages are all fresh as of yesterday or today but not all of these can be attributed to the changes I made on the home page or sitemap this week. Strangely, my sitemap has been changing back and forth between a gray and a white bar since the update started - and still is.
Not for optimization purposes but trying for better content, usability and quality, I have been making changes for two months by switching to CSS for everything but positioning, many changes to the body content, titles, alt tags, nav bar, file naming conventions and H tags. All the things I thought were the reasons for being penalized were taken care of at least a couple months ago. The site is still the same basic design and nav structure as it was last year, but has been tweaked a lot to make it cleaner.
Finally, I checked my logs and googlebot was around early this AM and did 'get' some of these newly listed pages, but she didn't get all of the ones that are now listed, <added> Since I started writing this, more internal pages are in :) :) :) </added>
Thank you Ms. Googlebot!