Huge frame counts are normal for long animations like this. A minute of animation is 900 frames at 15fps, 480 at 8fps, 1440 at 24fps (in reality it’ll be a little less, as frames where nothing is moving can be represented as a single frame held for a longer time). I only really do gamedev animation, and even when animating cutscenes, I try to avoid doing this sort of storyboarded animation if I can, precisely because it’s so much work!
You can use tags to stay organized, by labelling scenes and the shots within them. Using shot tags also lets you preview that shot more easily.
If the timeline is getting unwieldy, consider splitting off each scene or even each shot (for the longer ones) into separate files. You can stitch them together later in a video editor when you do audio. If you do this though, I recommend doing your initial blocking in in the previous shot’s file before splitting it off, so you can check for weird alignments between shots before you animate too much of the new scene.
It’s currently not very convenient to manage large numbers of frames because Aseprite gives you no way to collapse tags.
For large animations with a lot of frames, Aseprite can also run out of memory, which is another reason it’s better to utilize several files and stitch the outputs together later.
There are some scripts to make some of the work less tedious, have a look in the Scripts section. There are scripts that’ll make rough tweens for you, scripts that’ll move objects along a path, and probably some others.
Aseprite also has a reference layer feature, you can use this to import your story board while blocking out scenes. I don’t think the reference layer itself can be animated, so you can only have one board frame at a time, unless you have a different file per shot.