QWEEDDYZ: Reinstall GOG standard offline version.
There is Q2Launcher in game folder and
ini file for it. Change ini file qake2 executable to ymagiq2.exe.
YamagiQuake2 is source-port mod. It require base game. there is no need to manually tweak nay game files - base game pack loaded proprely as is. As well as for addons.
If you also additionally install any content mods wit new folders - you can add them to ini file as new entries.
Currently base game pack and addons question - it mean you dont have game installed. Creqte and copy files from gog game to new folder eg X:\Games\Quake-2x\ , put all game files there, and extract yamagi there. If you dont want to make any changes to cear game version. Or extract it to normal game folder.
For GOGGalaxy game version and GOG Galaxy client it is also not needed any tweaks. Just use same Q2Launcher.exe as Galaxy launch at game starting. Afyer proper changes to ini file you will see that Launcher show Launch 'Yamagi Qquake 2' instead of 'Launch Quake2'.
Just before installing yamagi verify game files in galaxy client if you installed it not from offline setup exe file
setup_quake2_quad_damage_2.0.0.3.exe is offline installer
GOG_galaxy_quake2.exe is online installer.
New laucnher should looks like attached image, but for differ source-port mod.
I have the game installed . I could not run the game without yamagi port. I have followed the instructions that are on the forums. Therse were files that Ihad to be odeleted and of course I downloaded and extracted files from yamagi web site. Than an error occurred, It was dealt with be copying pak files from my galaxy quake 2. I launched the game with Yamagi Quake 2 and it it is working properly. Now I do not know how to run the expansions. The instructions also said that I needed to delete the Quake2.exe file in the folder that you are talking about. But I don't see the ini file.