To uninstall properly, go back in the geany-plugins directory you cloned, then run sudo make uninstall. Then, to get back the Ubuntu version of pairtaghighliter (if you want it), do sudo apt-get install --reinstall geany-plugin-pairtaghighlighter.
Then you can safely remove the geany-plugins directory and the packages you installed to build it (at least libtool and libgtk2.0-dev, but you might know which ones you had to install and which ones you already had).

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