jdancing - 4:50 pm on Jul 20, 2010 (gmt 0)
Earlier this year it seems you had some backlink gaming problems in Google's eye's. It seems you fixed things and you did a reinclution request and eventually got your site back in the index.
Then months later you do this massive site rewrite. I am thinking when you were reincluded to the index, your site was put on probation and when everything changed overnight you triggered a flag which pulled your site back out of the index because now Google is wondering what you are trying to do now.
Perhaps this code change scheduled your site for a manually review. If there is even one borderline trick you are doing now it could be a while before you see your former rankings again.
The backlink issues you had in the past definitely could be related to the problems you are having now.