Thanks for the answers.
You say it is a large site, but you are discussing it as if you are running a one man business. Do you actually have many employees, or is this your own solitary project?
Yes, I am a one man operation. I have continuously improved the site in every way since its launch in 1998. From content (all written by me) to site design (hired designers). I have always ranked well regardless of any updates. This one hit me hard and I have been scrambling to get back with no luck.
Some of the sites ranking above me are train wrecks when it comes to navigation and content. Ads on top, sides and bottom of the content pages and pop ups. I see domains with positions 2,3 & 4 for a term. Its just so frustrating without any real guide to go by. (Yes, I read the google blog but that was as clear as a bucket of mud.)
So the new algo wants to see:
People "hanging out" on my site?
Twitter links to my site to get the "social community" radar working.
Digg and other sharing sites to mention me and users sharing my content.
Random links to my pages from all over the world.
Not one page that is straight to the point, but instead pages that run on like a 8th grade student's book report.
I have put in countless hours reading, working and thinking, but this one is not making much sense.
@walkman - I hope this does not drag out much longer because (you are right) I can't afford that.
@synthese - Trust me, I'm there.