You're welcome! I'm not aware of any registry settings that would need to be removed or modified. The few registry entries that FactorLib uses (I see 8) are for most recently used file locations, communication ports, and window geometry. I'd guess they are common to all versions of FactorLib and so are likely still in use.
Just as a disclaimer for anyone else reading this thread, and I'm sure you already know this, manually editing the Windows registry can quickly and completely mess up your computer. If you're not absolutely sure what you're doing, my best advice is to leave it alone. Overall, it looks to me like Eventide's done a really good job with FactorLib not leaving a lot of junk around, either with registry settings or shared files. It's much cleaner than most installs I've seen, so even though there's no uninstaller with the older versions, there doesn't seem to be a real need for one, either.