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In that time, the rankings improved slightly, but it also resulted in a drop from PR 5 to PR 4 on the home page. This is understandable because of the "bad" links that were removed.
Since then we have made several improvements to the site:
This has all paid off and 3 weeks ago (about 6 months of work) resulted in a huge traffic boost with improved rankings in Google across the board. Then, last night, the home page PR dropped again from PR 4 to PR 3. I've looked at the SERPs and our rankings remain strong.
The question I have is why does the PR continue to drop? I'm building high quality links from pages with a good amount of PR. We've also redirected a lot of the old wasted PR to the home page. My initial thought was that during the restructure, we didn't link the site correctly and lost PR that way. But through all my reading, the site is linked correctly to take full advantage of the PR possible with the site. Should I be worried?
Google's 3-card Monte game with TBPR may be something worth noticing, but it's not worth any concern if you are still getting the well-targeted search traffic.