installation should be
wfa-client.exe
\baseq3\pak0.pk3 (and maybe the other pk3's)
\wfa\pak3.99a.maps.pk3
\wfa\pak3.99a.pk3
\wfa\pak3.99a.vm22.pk3
You should be just able to click on the wfa-client.exe and it'll fire up wfa.
if you fire up ioquake3.exe by itself without any updates, it'll do the id intro AND you need all the files from the point release. http://www.fileplanet.com/61607/60000/fileinfo/Quake-3-Arena---Point-Release-%28v1.32%29-Final
This is because ioquake3.exe, by itself, is looking for baseq3 files, and is basically a point release executable and looking for the point release stock pk3's.
wfa-client.exe is basically firing it up with +fs_game wfa.