I caved and bought a 16oz jar and I’ve already added Naptha to start the pulling process but I’ve realized with how big my jar is that separation layer is very hard to make out, is it safe to dump all the contents of my jar into a smaller one or should I just suck it up and deal with the larger one?

Best to use a wine bottle or something similar if you're going diy. Basically something with a slim neck from which you can collect the organic layer from.

Ps. Use a glass pipette. Depending on what solvent you use a plastic pipette may not be suitable. Some hydrocarbon solvents dissolve plastics.

I bought a candle in a long narrow glass just to use it for this application. It is 20 cm high x 5.5cm ID.
it perfectly fit the filtered basified fluid from 100 grams of bark. Makes pulling naphtha easy.