I would like to move the Vorbis stream into an ogg container but ffmpeg does not seem to recognize the stream.

Even though MPlayer gives this output upon playback:

Opening audio decoder: [acm] Win32/ACM decoders
Loading codec DLL: 'vorbis.acm'
Loaded DLL driver vorbis.acm at 10000000
Warning! ACM codec reports srcsize=0
AUDIO: 44100 Hz, 2 ch, s16le, 128.0 kbit/9.07% (ratio: 16000->176400)
Selected audio codec: [vorbisacm] afm: acm (OggVorbis ACM)

ffmpeg:

ffmpeg -i Source.wav -acodec copy Target.ogg

Input #0, wav, from 'Source.wav':
  Duration: 00:02:15.17, bitrate: 128 kb/s
    Stream #0.0: Audio: qg[0][0] / 0x6771, 44100 Hz, 2 channels, 128 kb/s
[ogg @ 00000000003096C0] Unsupported codec id in stream 0
Output #0, ogg, to 'Target.ogg':
  Metadata:
    encoder         : Lavf53.6.0
    Stream #0.0: Audio: qg[0][0] / 0x6771, 44100 Hz, 2 channels, 128 kb/s
Stream mapping:
  Stream #0.0 -> #0.0
Could not write header for output file #0 (incorrect codec parameters ?)

Of course this does not necessarily need to be done via ffmpeg, any method that is workable would be fine...

I have cut down one of the files to 512KB: sample.wav
(Changed two chunk size fields in the wave header to account for this, the embedded stream is cut "without notice")