Sounds like you're ready to go! I don't have much experience with time lapse plants, but I do with other stop motion video. You're using a GoPro. Do they have a stop-motion feature? How cool.
I'd recommend in the future using a photography camera with an intervelometer. GoPros as far as I know all have a serious fisheye effect, which might distort your flower. If you have a digital SLR camera it will also give you specific controls for much better light control. Since the camera's not moving and the light doesn't change you can do all kinds of things with aperture and shutter speed without making any compromise in the ISO settings.
Of course the GoPro has the advantage of being small for nestling in with plants as well as being water resistant. Plus, I imagine they have a better battery life if an outlet's not near by.
If stuff gets moved during it might be better to switch completely to a different angle rather than try to recreate the exact image. If possible though fix anything and everything in place with screws, duck tape, sand bags, whatever you have. In my experience anything that can move, will.
P.S. I'm a little jealous. I can take stop motion and grow plants, but can't grow plants were I can take stop-motion. Best of luck. I'm excited for the results.
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