I'm currently in the process of doing an extraction from 350 grams of Peganum Harmala seeds. I ground up the seeds to a fine powder and then boiled the seeds for 5 or 6 washes with a dash of vinegar, combined all the liquids and filtered them. I had about 7 liters of tea which I reduced to 3 liters before filtering again, reduced to 1.5 liters and filtered again and then reduced to 500 ml and filtered for a last time.

After this I added lye. While pouring a large clump fell out of the bottle into the solution so I believe there's an excess of lye in there. After I let the whole mix settle over night it turned into a sludge with no precipitations in the bottom. I hypothesize that the large number of plant oils in the mixture turned into soap and made it impossible to reclaim the harmalas. I diluted the solution, stirred and overnight I saw precipation form in the bottom. However, after letting it rest a large dark column of liquid is floating on top.

What is this? And is it possible there are more harmalas trapped in that layer? I managed to pour of most of the dark liquid into a separate container but disturbed the precipitation in the bottom. So both containers now have a layer of precipitation in the bottom.

Any ideas what's going on here?

Your results are normal for this method.

I have extracted many lbs of syrian rue doing this. It is advised to first allow the solution to rest for a day or so to let the goopies settle out. It is also advised to filter the boiled solution very well(cotton balls) before adding base it does seem to effect yields. A note on this step is to change the cotton balls out as soon as they get clogged. Towards the end of this process it may take many changes of cotton balls, otherwise you'll be waiting for days to filter.

Here's what to do next. Decant the top black solution as much as possible, be warned though this precipitate is pretty 'fine'. Meaning that its easy to lose some product decanting. So decant a bit to save time then filter the rest. Keep that precipitate note this is full range syrian rue alkaloids, they can be eaten as is but I recommend purifying further.

Sometimes, not always, but sometimes, you can add more base to this black solution and more precipitate will be formed. It's best to wait a day after another addition to see, don't be disappointed if nothing more comes out of it though.

Once you have a(or multiple) coffee filter(s) or filter paper(s) nice and clogged with this stuff instead of waiting for it all to be dry or whatever you can simply add an acid such as a citric acid solution or vinegar. I usually used diluted vinegar because this stuff is pretty soluble in it as is. I prefer to do this step hot or warm(really improves the result) but room temperature is fine. A microwave can warm a vinegar solution in a minute or two maximum. Feel free to poke a hole in the bottom of the filter paper and scrape the sides of the filter paper while pouring the acid to get everything off of the filter. Just a quick time saving step of getting the 'full range' to a salt in solution.

Now you can do another acid base to clean things up or a classic manske. Or a few repetitions of both. I prefer to start with a manske. The results are beautiful because the solution is so concentrated(easy to get 30-40 grams into two small mason jars or flasks). If the Manske is done while the solution is still warm and allowed to cool(after salt addition) one can watch a red/brown solution turn completely to gold hydrochloride salts. At this point I usually would filter and rinse with cold concentrated salt solution(over vaccuum). The manske is usually about 90% done in 2-10 minutes, but you can wait longer if you so desire and are very anal about yields. I find stopping purification where the alkaloids have a gold/tan/pink hint is best for a completely effective compound and keeping a healthy yield.

A little side note. I actually preferred this method because it got me straight to the alkaloids for 'purification', used a lot less water, energy, and the rue tea solution doesn't necessarily have to be boiled down. I suppose if I were to extract again I might make some minor revisions to this but when done correctly with potent seeds it can yield a wonderful hockey puck or two of alkaloids. The yield after purification may be slightly less then the yield of other methods but I have received a 7% yield without using any solvent doing this. For the work and time saved I'll take a cut on the yield, Syrian rue is very affordable.