The thing about scripts is: they keep running even if you remove the script file. Seems like they're cached somehow. So if you want to uninstall a script completely, you have to first remove the script files and afterwards stop ALL instances of the running script. Usually, this can be achieved by issuing a stop command to all ships/stations running the script. Global scripts are a bit tricky, though as there is no instance running the script.
I am pretty sure, though, that there is a way to stop particular global scripts. I only have forgotten about it by now. Google might be of help.
Regarding compatibility with my MK3 scripts ... sorry, no idea at ALL anymore. Even if I used to know about this one, I have forgotten by now. It's now just too long ago
The Reunion MK3 script was some sort of ripoff of the AP one anyway so I'd actually recommend playing AP as only there you're able to enjoy MK3 traders at their best, including sector blacklisting and stuff
I hope, this is of any help for you ...