I'm seeing a different sort of issue and approach here: something that was done in Cubase--which I had a copy of about ten years ago--where audio peaks or "hitpoints" could be aligned with a midi file essentially by adjusting the TEMPO map. I think there's something more or less equivalent in most midi software, these days.
Not the same thing, btw, as the function in 8.5 which allows you to "tap" in the tempo in a way that actually modifies the tempo map from beat to beat. (Useful, but not pinpoint accurate.) The old "hitpoint" in Cubase approach allowed a dead-on accurate beat by beat manual adjustment of a midi tempo track to fit an audio track.
Probably old ground, here, but does Cakewalk now have an equivalent? (I think the modern equivalent in Cubase is called "Warptool" or "Audio Warp" or something along those lines.)