We have a site that used to be in a subfolder of another, unrelated site. But this unrelated site was loved by Google and we had thousands of terms that ranked #1 or #2.
But Google caught on after a number of years and actually penalized this 1 folder, and all our rankings dropped to about page 6 in the SERPs. The rest of the site still ranked very well, the penalty was definitely on just the one folder.
So we 301 redirected the entire site (about 7000 pages) about 5 months ago to a domain that I had owned for years. In our Google sitemaps account, Google now says that they have about 6000 of the new pages cached.
Now this new site ranks as well as the old one for a handful of terms only. Some of these great rankings are for extremely competitive terms that have millions of results, yet we rank #1.
But this is only the case for 5% of the terms, the rest seem to be cached by google but don't rank at all, not even in the first 100-200 results.
I have looked to see any commonalities among the pages and inbound links of these well-ranking 5%, but I find none. Some have no inbound links from other sites, others have many. There seems to be no rhyme or reason. When I checked the inbound links, I used Google and Yahoo both to get a more complete backlink picture. The on-page factors are relatively the same among all the pages of our site as well.
So . . .
What could be causing this handful of phrases to rank the way they used to before they were 301 redirected?
What can I check to determine the difference (in Google's eyes) between the 5% that are ranking great, and the 95% that aren't ranking at all?
Why aren't all the phrases ranking the way they used to?
And how can I get the other pages to rank the way these 5% are?