OK, if you started over anyways, don't delete anything. It's the safest.
Unless you want to know some more details and unless you are prepared to get confused
... stop reading now
...
If you don't delete then the only thing that can happen is that you may just be confused about having 2 or 3 exe's (wq3_02post.exe and wquake3.exe) - use wquake3.exe (from now on, I will simply overwrite the exe anyways).
Ignore the MacOSX and linux stuff (which may also have 2 versions now : Linux: linuxquake3_02post, wquake3 and wq3ded - MacOSX: Quake3.app and Westernuake3.app)
Also, when I wrote "delete Westernquake3\pak0.pk3" I meant exactly "Westernquake3\pak0.pk3" and in particular I did not mean "Westernqauke3\baseq3\pak0.pk3" !
... (I know, I tend to be brief ...) But if you downloaded the latest version of wq3_b21_sa_testpatch01.zip you should not even have Westernquake3\pak0.pk3 - and even if you do, with wq3_b21_sa_testpatch02.zip it does not matter anymore.
Another thing: extracting the patches from
http://www.westernquake3.net/viewforum.php?f=19 should be done inside "Westernquake3/westernq3" (in analogy to "Quake III Arena/westernq3")
Lastly: sorry for answering rather late