You have scenes and sequences that are interesting but aren't adding up to a coherent whole. One reason for this may be that there really wasn't a clear story to begin with. What you can do at this point is take a step back and return to the earlier stages of the process. Knowing what you know now, try to write up an outline that identifies what the story is, what the train is, whose story it is, what the key moments are that you're driving toward, how the story is resolved, and the key points you hope the audience will take away from the film. Then look at your material with this information in mind and see if you have what you need. You may need pick-up material to fill in the gaps, but you also may be surprised to find that you are heading in the right direction, and just need to do a bit of housekeeping.
For example, you may have to drop favorite scenes because they don't serve the story that you now realize you're telling. If a shot or a scene or even a sequence is a distraction rather than an addition, it's got to go, no matter how expensive it was to shoot or how difficult it was to get. You can spend some time trying to fiddle with it, see if you can possibly make it work, but, ultimately, if the material is beside the point, it goes. The same standard should be applied to interview material. If you didn't plan ahead but instead simply shot a few available experts, it's very possible that there will be redundancy and somebody's interview will be dropped. (If you end up cutting people out of a show, do them the courtesy of letting them know before the program is aired.)
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