Two suggestions:

First - Use a beaker/jug shaped container so that after you agitate the solution, the naptha winds up in the neck of your container.  This creates a greater depth of naptha and less propensity for you to suck up your basified rootbark solution.

Second - Use a smaller baster or pipette as the volume of your naptha decreases.  In his initial extractions SWIM would use an eye-dropper to get the last 25-50ml without any black liquid.