The short version is:
- Import the clip, and verify the first beat is at 01:01:000.
- Set tempo to 85, and listen for a few bars with metronome on to verify sync.
- Go out to bar 45, and listen for where it goes out of sync (after 45:03:000)
- Set the Now time at 45:03:000, hit Shift-M, and set the meaure/beat so changes after the point won't average all the way back to the beginning.
- Listen to and the rallentando section, ignoring the out-of-sync clicks in the track, and pick out a few other piano notes with obvious transients in the waveform (I didn't bother to enable Audiosnap, just picked them out by ear and eye) and use Shift-M to set those points (with the Now time on the transient) to the correct measure/beat (note that partial beats are decimal fractions, not ticks).
- Since hte musical hit at 47:01:000 comes in early, you have to set the last preceding musical note at 46:04:000 so that when you set 47:01:000, it doesn't average tempo back to 46:03:480 (beat 3.5) and mess up the end of the rallentando.
- Set the tempo to 100 at 47:01:000, a verify the rest of the piece follows it as advertised.