I don't think I've ever animated with Illustrator, per se.
I might create multiple artboards if I needed to do cells.
Otherwise, I might have one master file with all of the elements.
...just some general thoughts.
Did you make any progress with this?
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I actually put it aside due to work load. I do remember creating the animation by using different layers for each movement, then using automation (years ago!). When I get some time, I'm gonna give it try.