Yes - thanks for all of your help with that. TSMUXER is what’s fixed it for me in the end. So after I’ve repaired episodes one and two, I’ll spend a day watching Always Sunny and running all my sources through that for video and ffmpeg for audio.

Unfortunately as to your nitpicks, I’m using the longest possible shots there. It’s one of the things I’m meticulous about - I cut the longest possible shots out of the track, to give myself the most possible to play with, then I trim them down if needed. So I think that that version of the sequence is as good as it can be. And as you say, it’s no worse than Clone Wars’ slightly less-than-perfect standard, so I think it’s forgivable.

I don’t feel like the music drops, though - and looking at it, that is the original track which played there. But I don’t think it warrants a repair.