Yeah, when you've identified the end of the VOT (with positive VOT, anyway) you've also identified the start of the vowel. You then need to go find the end of the vowel which I normally take to be the last glottal pulse that has the same basic waveform shape as the vowel had near its midpoint. I highly recommend using a textgrid when you do this. It makes it much easier to set your boundaries carefully and then, if you need to, go back and see exactly what decisions you made during those measurements. The most important thing is that you be consistent in your decisions. If you start off by marking the first zero crossing before the waveform goes positive and the second zero crossing after the last glottal pulse returns from its negative phase then do that for ALL of them. Finally, I HIGHLY recommend Will Styler's excellent intro to Praat: wstyler.ucsd.edu/praat/

me too!