The original MV2H metric was designed to evaluate systems which transcribe from an input audio (or MIDI) piece to a complete musical score. However, it requires both the transcribed score and the ground truth score to be time-aligned with the input. Some recent work has begun to transcribe directly from an audio signal into a musical score, skipping the alignment step. This paper introduces an automatic alignment method based on dynamic time warp which allows for MV2H to be used to evaluate such non-aligned transcriptions. This has the additional benefit of allowing non-aligned musical scores---which are significantly more widely available than aligned ones---to be used as ground truth. The code for the improved MV2H, which now also includes a MusicXML parser, and allows for key and time signature changes, is available at www.github.com/apmcleod/MV2H.