idolw - 9:12 am on Jul 13, 2010 (gmt 0)
Regarding the navigation links... yes, I did add a site-wide navigation bar that did not exist before. It contains about 20 links to each section of my directory-based site. I don't see how that could trash things though. If anything, it makes it easier for googlebot to discover the other important sections of my site. Each section has always enjoyed it's own favorable results within Google.
This ends the case in my opinion. Some of your pages (including home page) were probably ranking basing on lots of internal link love from internal pages. Now, when you have added 19 more links (I bet optimised for anchor) the home page receives way less link juice.
I would try to re-think the navigation to limit the number of new links so that link juice is not so hardly distributed.
Or wait for Google to figure everything out as Matt Cutts suggests.