You probably have wayyyy too much liquid for that amount of bark. 1 liter is more than enough for base mixture + naphtha. You can't see the naphtha because you're using such a large container that the layer becomes very thin. You want the narrowest jar you can still siphon from so that the layer is at least a few cm thick.
Here's a course of action to fix your situation:
* Acquire several 1 liter glass jars with lids of a similar shape to the attached picture. You will want both a wide lid for easy siphoning (>4cm) and a narrow section near the top.
* Acquire a way to accurately siphon the top layer off - either a glass turkey baster or a glass syringe, syringe if possible.
* Fill each jar around 90% full with the base mixture, leaving some room (i.e. <100ml) for naphtha.
* Fill the rest of each jar with naphtha.
* Rather than mixing the layers with a spoon, a much safer and more efficient way is to put the lid on the jar(s) and gently rock them each for 5 minutes.
* Siphon the top layer from each jar, being careful to not suck up any of the black liquid. Combine in one container.
* If you get any black stuff in your siphoned naphtha, just siphon the naphtha off that container into another, the black stuff will sink to the bottom.
* Freeze precipitate the clean naphtha.
arcologist attached the following image(s):

jar.jpg
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