How to obtain a mixed stave of two identical loops with different tempo?

(This is the short explanation)
Is it possible to obtain a mixed score of two identical loops with different tempo?
I have a sequence of 12 16-th notes that I play at 96bpm, and the same sequence of notes that I play at 97bpm, both in loop. The result is that in the beginning we have a unison and after a bit they start to unsync.
I have already both MIDI files, but I'd like to obtain a mixed score (with one stave for voice a and one score for voice b, to get a musical idea of how exactly they are syncing and desyncing.
Anybody can help me?

(This is the long explanation)
- I'm processing Reich's Piano Phase (please skip this part if you know the piece). It's composed of a) a sequence of 12 notes that should be played in loop at approximately 72 dotted quarter-note per minute; and b) an identical sequence loop that will start in sync with the first one and slowly accelerate thus dephasing from it. This is sumarised in the original score, where it shows that (excluding the 1st measure) both voices start in sync (as in 2) and after a while (depending on the accelerando) they will be as in measures 3, 4, and so on.

- I'm simulating this in PureData (except for measure 1, where only one sequence is being played), where I generate both MIDI tracks procedurally: track 1 corresponding to a) generating a 16th-note every 138 ms (which gives roughly the 96quarter-note-per-minute); and track 2 corresponding to b) generating a 16th-note every 137 ms (which gives roughly the 97quarter-note-per-minute).
- I don't give explicitly any indication of tempo or any header information for the MIDI file, and Reich explicitly avoids measure-related metric information, because he wants the musicians to avoid all musical accents. Nevertheless, we could assume a 6/8 measure by looking at the original score.
- Finally, I generate 2 audio tracks, mix them, and then I perform some computational analysis on this resulting waveform. My goal is to be able to show the full computational analysis (in a report) of the 6/7mins long and be able to focus on specific areas and show the corresponding "stage" (like in reich's score measure 2,3,4,...). Ie, I would have a plot where I have the computational analysis (produced in Python and shown in a real time scale - miliseconds) stacked upon one stave for voice a) and one stave for voice b). Ideally, these 2 staves would be as similar as possible to the original (although not necessarily with the 2 voices on each stave - some 16th-note are upwards and others are downwards).

Does anybody know of any way I could accomplish this (with or without MuseScore) ?

Thx in advance.