Determine similarity in percentages between species A and B, A and C, and B and C
Step number one is correct, but note that there are several similarity (or alternatively distance) measures. What you choose is the simplest and most intuitive one and it a good one without any other assumption or explanation given.
Step number two is also correct, if the similarity is a good proxy for when the last common ancestor between two species is in time, which in this case should be.