Hidden issue within my multisite installation

My original site was an old multi-site setup. On my first server everything worked fine. Move from Host Gator over to GoDaddy quite some time ago, everything remained fine, but in order for it to work at all I had to do an old multisite install and then upgrade to WP 3.0 and so on. Then I upgraded servers within GoDaddy from a shared server to a virtual dedicated server. I was told I no longer needed to do the install of the old mutlisite software and then the upgrades like I did previously to get it to work. Since then something is seriously wrong with my wordpress install.
Our busiest site was steadily growing, traffic was climbing higher and higher, it was producing revenue from ads, until that switch that is. Since then new posts and keywords never show up in search statistics, the entire site has gone stagnant, there has been zero growth on every front. The only things that do show up in search statistics (checking multiple stat programs and all the same result) are the older keywords from up to 2+ years ago. The site has just simply died out for no good reason. The audience is still there, its not like the topic of the site suddenly became uninteresting and unpopular. Something in the site setup has to be amiss.
Since moving to that virtual dedicated server we were also hacked once and had to rebuild from a backup on a brand new virtual dedicated server. Things got even worse after that move, which was in March, 2012.
Does anyone out there have any ideas why? Are one of the experts around here willing to come take a look at the setup? I am desperate for some help. My entire network is just shriveling up and dying.
My main site is: http://www.worldblogosphere.com
The busiest site that I mention is : http://www.extraordinaryintelligence.com

Thanks for any help,
Gene