Yes, there is a thing called too much naptha.
As stated above, your problem will be freeze precipitation. It can be confusing, because anything your naptha evaporates from will smell like DMT but you'll have no crystals. Low amounts of naptha mean higher saturation and easier precipitation.
A narrow extraction vessel is one way of dealing with small volumes of liquid. The naptha layer will be thicker and easier to pipette up. Lab pipettes, eye droppers, siphons, and other improvised tools will work better than a turkey baster or trying to pour it off.
"The mystic cannot communicate, but the artist can." ~Robert Anton Wilson