Unfortunately, the analysis tool used to create a permutation of Super Mario has ultimately led me to a dead-end. While such analytic methods might help for basic applications such as chord progressions, they clearly don't work as well when applied to individual notes, since duration, velocity, and padding must also be taken into account.
If I had the time to develop a more comprehensive analysis tool that used more than just a first-order transitional Markov matrix, I might extract better results from this analytic method. I feel, however, that this would simply take too long. Such intense analysis would merit an entire thesis all of its own.