Phew. Finally, our SharePoint sites should now be back to "normal". Because we basically re-installed SharePoint on both servers we needs to add back the ability to index and search Adobe documents ( ie PDF's).
By default SharePoint will do Microsoft files like Word and Excel but to index PDF's then you have to install some software from Adobe, then make some configuration changes (read registry hacks) and finally do a full re-index of the site to incorporate all the existing PDF information in SharePoint.
We have now completed all those steps so this SharePoint ( http://supportweb.ciaops.net.au ) and our internal SharePoint site should now be back to exactly the point before the application of the recent patch.
In thanks I'd like to offer a quick prayer : Our Father who aren't in heaven, please don't let this happen again. PLEASE.