My SWF has also seen very decent reductions in volume between syrian rue and a manske extraction (not using vinegar at all). SWF thought that EtOH would get most of the NaCl, which she thought the major contaminant, but the results did not end up all pretty as expected, thus contaminants were suspected.
Converting to base form - could this be done via sodium bicarbonate or sodium hydroxide/potassium hydroxide? As for 'washing with cold water' would it really matter if the water was at 25-35 degrees C as is most tap water? I suspect that it might help to extract the bases into a non-polar solvent, DCM or naptha as you desire, as to ensuring no little bits got lost. Also even a filter would miss some of the base that comes out - a nonpolar, given time, would ensure that you missed none of it.
Would harm(al)ine freebase be more or less stable than the salt as regards to oxidation? Would a simple solution in - say - vodka - of this resultant freebase as resultant (mr gnrm23, where dost though getest thine ammonia from, those who make stinky-way wizzer would surely be curious) - pardon me, would it be possible to put the freebase into ordinary vodka type alcohol (whisky/gin/etc if you wish) and would this keep it longer (especially if stored in the freezer)?
questions questions, it is all I have isn't it...