We present a corpus of virtual patient dialogues to which we have added manually annotated gold standard word alignments. Since each question asked by a medical student in the dialogues is mapped to a canonical, anticipated version of the question, the corpus implicitly defines a large set of paraphrase (and non-paraphrase) pairs. We also present a novel process for selecting the most useful data to annotate with word alignments and for ensuring consistent paraphrase status decisions. In support of this process, we have enhanced the earlier Edinburgh alignment tool (Cohn et al., 2008) and revised and extended the Edinburgh guidelines, in particular adding guidance intended to ensure that the word alignments are consistent with the overall paraphrase status decision. The finished corpus and the enhanced alignment tool are made freely available.