Is there a comprehensive list which enumerates how many times they argue - and what those instances are?
We have testimony from Rambam himself about this. Towards the end of his introduction to his Commentary on the Mishnah, Rambam writes as follows:
וההלכות שעשה הרב הגדול רבינו יצחק זצ"ל הספיקו במקום כולם לפי שהם כוללים כל תועליות הפסקים והמשפטים הנצרכים בזמננו זה כלומר זמן הגלות וכבר בירר בהם כל השגיאות שנפלו בפסקי קודמיו ולא הוקשו לנו בהם אלא הלכות מעטות לא יגיעו לעשר בשום פנים
And the [book of] Halachot that the great rabbi R. Isaac of blessed memory produced is sufficient against all of them, for they contain all the benefits of the rulings and laws that are needed in our times – meaning the time of exile. And he already clarified all the mistakes that accrued in the rulings of his predecessors, and we have difficulty with them only on a few laws – not even reaching ten in any form.
If we assume that having difficulty with a ruling is equivalent to disagreeing with it then at the time of the writing of the Commentary to the Mishnah he thought that he disagreed with the Rif fewer than ten times.
However, in a responsum to R. Nehorai ben Hillel the judge, Rambam wrote as follows:
אמנם מה שזכרתם על רבנו יצחק ז"ל בזה המקום הוא זולת מה שאמרנו בלי ספק והיא דבר בלתי צודק אמנם לא ידעתי אם אמר זה ר' יצחק ז"ל או לא וזה שאנחנו חלקנו עליו בקצת מקומות כמו ל' מקום או יותר מה שתפס עליו תלמידו רבנו יוסף הלוי ז"ל בשבועות ובבתרא וקצתם הערנו עליהם
However, that which you mention about R. Isaac of blessed memory in this case is without a doubt not what we have said, and it is something incorrect. However, I don't know if R. Isaac of blessed memory said this or not. And this that we disagree with him in several places – about 30 or more places – that which his student R. Issac the Levite of blessed memory grasped against him in Shavuot and [Bava] Batra, and some of them we have commented on.
Here he seems to think that he actually disagreed with the Rif around 30 times. This could either mean that the statement in the Commentary wasn't referring precisely to disagreements, or that in the years since writing the Commentary he revised his opinion or had more disagreements. (The latter is the suggestion of R. Sheilat in his footnote to the responsum.)