Things finally clicked this week. I now understand how to deal with the multitude of codecs, formats, and sizes so there is consistency in footage and good function with Final Cut.
Encode everything as ProRes 422 using MPEG Streamclip in either 1080p or 720p. No more, no less. Export whatever, but for Capture Scratch have footage that is only ProRes 422 1080p or ProRes 720p, period.

Song is "King's Blues" by Big K.R.I.T.

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