The
Template Modification System hack seems ideal for hack with so many template edits, like this one. If anyone has created the Template-Modification XML file, for the Thread Prefixes add-on, then please post this here. This will save a lot of work for many others and will keep your template changes through upgrades of vbulletin and the Thread Prefixes add-on.
Edit. I was just informed that the XML file is included in the zip file of the
Template Modification System hack, so that will make installing Thread Prefixes a piece of cake.