If the number of files didn't increase, or increase very much, between it working OK and getting slow, then it could be something else.
Synchronize, like Flat View (Grouped), will display all the files at once, which potentially means things like 3rd party shell extensions are called on a huge number of files, and files of lots of different types. If there's a problem with a particular shell extension (or with code in Opus, which can also happen) and a particular file, it could be that causing a delay, and Sync is only really involved because it's triggering that file to be displayed. If you think that might be happening, the best thing is to try and narrow down if the slow-down only happens when certain folders are included/displayed.
Re FolderMatch, I don't know if anyone has posted a pre-made way to integrate it, but most file/folder comparison tools work quite similarly, so it's usually pretty easy to do.
This post has a script/button which handles integrating various similar tools: