I didnt read the Gordo TEK, but maybe this should still help:
If it is completely clear, then all the goodies that precipitated must have settled.
If it is milky - then there is still material precipitating and not fully settled.
Therefore in your case just remove it. But as told: Don't throw your stuff away directly, let it also evaporate OR put it back in the freezer OR reduce it further and then put it back in the freezer (after decanted from your crystals). If you did not use any excess amoutn of Naphtha then it is very unlikely that the solvent should contain goodies after decanting, but better be safe.
Other question: So you mean that you just add bark and Naphtha to a pot and cook it, instead of making an additional step with a water cook at the beginning?
If this was the meaning, then there will not be any desired amount of goodies going over into your Naphtha.
I think it was mentioned that DMT is bound in the bark in form of a Tannate - a salt also containing any kind tannin. This will not come out just upon exposure of bark to the non-polar-solvent.
This should not grant any worth amount of product and also you would have to install a reflux apparatus, as otherwise your naphtha is going to evaporate really quick