Made vowel parallel to consonant and separated scoring from transcription for "other" sounds

Several somewhat major revisions that motivated by discussion in cross-site analyses meeting on 2014-04-28 and follow-up discussions in 3PIs meeting on 2014-04-29, etc.  Specifically:

# 09) vowel transcription changed to parallel consonant transcription
# 10) transcription and scoring separated for non-canonical substitutions
# 11) category of "unclassifiable" added to both C and V transcription
# Left to do:
# If we decide to adopt this strategy, should add way of making the correct transcription
# be the default choice at each of the two steps.