The downloadable oggs were higher quality as I remember.
I can see about reuploading them. However, the 1.08 soundtrack's new adds (Green Hill, Red Volcano, Verdant Forest, Aerial Garden) I don't have in the higher quality format.
As for extracting the songs. If you are okay with using a command line program, get LumpMod from
http://www.thunderpalace.com/software/lumpmod.html and read the included HTML file to figure out how to use it. The syntax should be something very simple, something like "lumpmod music.dta extract O_MAP01M GFZ1.ogg" for GFZ1's music.
If, like many people, you are command line shy, DeePsea will work. You can get it from
www.sbsoftware.com. I believe what you have to do is press F7 and look for something in there that says "examine," "extract," or "export." The downside here is I can't explain exactly what to do with it since I don't remember. While less efficient in this situation, command lines are faster for adding or modifying a single lump, so I usually use them.
You can figure out what music lumps of the form O_MAPxxM correspond to by looking here:
http://www.lawrencegearheadz.org/~a441/text/newmapheaders.html#musicslot
I made that document for a different purpose, obviously, so just pay attention to the list up to 108. Also note that 100-108 on the list correspond to O_MAPA0M through O_MAPA8M.
The O_ lumps are all encoded with Ogg Vorbis, while the D_ lumps are alternate versions as MIDI files.