Decorate the Bottle
Get out your heat gun and cut a bunch of strips of fantasy film. Layer the film over your bottle and gently hit it with the heat. Watch it shrink and bond around your bottle. (Man this is fun.) Put a bunch of layers on until you're happy with the diffusion.
Cut a bunch of strips into your leather scraps and artfully wrap it around the bottle, tying and gluing as needed. I left a few long strips and a loop at the top so I can carry my bottle around with me easily, or hang it from my belt.
Once you're happy with the bottle, carefully stuff in the guts. Start with the LEDs (be sure they're facing inwards, for more diffusion / glow), then the teensy and resistors, then the battery and connector.
Leave the 3 charms and the lock and key outside.
Put the key in the lock and be sure everything's still working.
Hide the Wiring
The other purpose of the leather wraps are to hide all the wiring, so your bottle looks purely magical.
Place your charms on the outside of the bottle and glue them down, strategically placing the wires behind the leather.
Finally, add strain relief and hide the wires to the lock and key with more leather strips.