Best way is indeed download 3rd party content, but better - whole game cd's. Mac or Linux fine too.
You need CD for Quake 2 with 10 tracks and Ground Zero with 5+5 tracks.
Better mount them and keep mounted during game (Ground Zero for addons)
Then grab it using ITunes, WMP or VLC to lossless. But that you can use only with sourceport mods. As i know WAV\etc isnt supported by any, the only they support for *lossless* is flac.
Cant say how, but seems GOG properly set which one tracks should be played. To do this in YamagiQuake2 sourceport, you need delete orginal ogg music folder, create music folders inside mission pack and put tracks there.
What is good for Yamagi, it can shuffle tracks. You can use one general music fodler if you want mix all 20 tracks for all mission packs or for Rechoning and Ground Zero only, while base Q2 will be ised music from baseq2 folder.
During gameplay i dont think it is a big differences in quality. Almost not noticeable. 'As is' music work in GOG as it should (seems like, 100% for base q2), 'as is' in Yamagi it shuffled all 20 tracks from one music folder in all 3 missionpacks.
For original Cds tech reference, main cue-files of images - you can use
http://redump.org/. Additional files for cue images - multi bin (each per track, 21 bin for Q2 Win\Lin\Mac and 21 bin for Q2 Ground Zero) can be downlaoded from somewhere as part of "redump-pc Q set" 's.