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.