If your site was working fine before the outage and now is not working fine ... I'd put the blame on something that Rackspace did in starting your site up again.
I'm not sure what query that is, but it appears to be getting portal settings or something like that. It looks like the thing that Tony Valenti used in the first of his recent tutorials on DotNetNuke performance. But, again, a change in performance that you see is most likely due to the changes that Rackspace made.
One thing that you can do to make sure that your database isn't causing a problem would be to truncate the EventLog and SiteLog tables. You should also backup your database and simultaneously truncate the database log files.
But
http://www.ironspeedmvp.com is running, although slowly. I was able to register and create an account, and I can login and logoff.
But, you do need to get Rackspace to treat this seriously and not blame DotNetNuke if it wasn't a problem before the outage