You don't want to use QTGMC for the entire thing, since it isn't a truly interlaced source.
You want to alter the frame rate. 29.97 is not correct. Most of this is normal, proper 23.976 that was telecined to 59.94Hz. Normally you would follow Telecide with Decimate.
As mentioned, there are random breaks in the telecine pattern as well as the other issues. It sort of looks like they started with a 100% pure telecine and then broke it during editing at NTSC rate, to shorten up certain sections. But the opening portion is actually slower than 23.976.
As for your most recent screenshot, that's one of the parts Colours was talking about where the chroma is "point-resized" in the source. I think the problem is actually that these parts use interlaced 4:2:0 instead of progressive, but Colours knows more than me.
Source frame 3560 [UtoY]
Source frame 3560 + nnedi3 [UtoY]
Source frame 3561 (good) [UtoY]
All you can do is mitigate the damage by making it soft instead of blocky.