I've just released an update to move this up to v1.3. I've also renamed it, as it's original name was with a different style in mind.
This update improves efficiency and adds AJAX username suggestion. It also allows for compatibility for vB versions before 3.7.0. The biggest improvement is definitely the template edit improvements. A lot of the link code was moved to the plugins that enabled the PM links, so templates weren't edited with as much stuff and therefore don't get messed up as easily now.
I'll add some instructions on how to add the popup PMs to a PM link outside of the ones that have been pre-configured with the installer on the first post of this thread. The installer gets all of the ones I know of that are default to vBulletin.
Let me know if there are any issues with v1.3, but it's getting to be pretty stable.