QUOTE
...but to avoid problems I should have selected the "The Legend of Zelda- Ocarina of Time Hyrule Symphony.cue" cue sheet?
Yes.QUOTE
Does this mean that, to be safe, after creating a repaired copy of my tracks, I should run CUETools' "Verify" feature on the repaired tracks?
I would. At least until you're confident it works correctly. QUOTE
How does the starting position have an effect on the bits that get copied to my hard drive?
Changes the CRC. The position of the data has changed within the frame by [offset amount] samples.