If your solution contains naphtha you probably shouldn't boil it down due to the fact that naphtha is highly flammable. Freebase DMT is not high temperature-friendly as it is in salt form, whether this will present issues whist it is in solution I couldn't tell you though.
In terms of good volumes to work at - I reduce my solution (whilst in acid solution) to 150-200mL per 100g bark used. I have found that at 100mL/100g and less I have run into an issue where DMT has crystallised and dropped out and back into the basic solution whilst I am in the process of pulling (I think that the naphtha may have become saturated and spontaneously dropped out the DMT).
If you have truly lost your naphtha in the solution you could add more. If your solution is too thick (it doesn't sound like it as you sound like you have too much liquid) then you can add more water or warm the solution in hot water to aid separation. Adding an excess of NaCl or more NaOH can also help.
As said before you'll find working at the basic stage easier in a thinner, taller vessel. You will also find it easier if you are using glass as you can view separation from the side which is impossible using a stainless vessel.