Tually, I just looked back at the song. I'm guessing you were smart enough to realize that tracks 2, 3, 4, and 5 (or 1, 2, 3, and 4 if you still use 1.34) are pretty much the "chord tracks" in that they contain pretty much just the chords with very little melodic embellishment. These tracks also have a lot fewer NCTs than the other tracks. This is partly why I chose ToT as the song to start analyzing, since not all songs have a set of tracks which serve exclusively as chord tracks. You may have been thrown off by the fact that, in measure 29, rather than sustaining the same note through the whole measure, the chord tracks change pitch on beats 3 and 4. A change in pitch doesn't necessarily imply a change in chord, and, in fact, the chord tracks don't change chord at all in measure 29, and don't even have any NCTs. Each of the three different sets of pitches are really the same chord with the notes in different arrangements.
A couple rules of thumb:
Most pieces of music have a fairly consistent harmonic rhythm. In other words, there isn't usually much variation in the amount of time between chord changes. The longest held chords are rarely held more than 4x as long as the shortest held chords. In ToT, for example, the duration of a chord ranges from .5 to 2 measures. When doing harmonic analysis, it is usually preferable to analyze very short chords, even if they are full chords, as NCTs.
Also, if you're unable to tell what a chord is by looking at the notes (maybe there are so many notes, you can't tell which ones are CTs and which are NCTs), the ears may be a better judge than the eyes. List multiple possible chord progressions, play each of them on the piano, and listen for which one most closely resembles the piece you're analyzing. If you don't have a piano handy, you can use some computer software (i.e. FL Studio, Psycle, pxtone) that allows you to treat the computer keyboard like a piano keyboard.
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