Highlight in four colours and work on those passages alone
Highlight what matters in yellow, lime, cyan or pink, then filter the transcript to one colour or several: everything else steps out of the way and you are left with your passages, each with its timecode.
Highlight passages in the transcript in four colours, then filter the view to one colour and work only on those.
Colours have no fixed meaning. They are yours: one for the parts worth clipping, one for what to cut, one for what needs a fact check, whatever you decide.
The filter is what makes them useful rather than decorative. Reading a forty minute transcript to find the eight passages you marked is the problem the highlighting was supposed to solve.
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