Ok so here's the deal... it's really much simpler than people are making it out to be.
First of all, if you have excess salt in your harmaloids, simply dissolve them in an acidic solution and re-precipitate them with sodium carbonate solution, just as phlux said. Trust me this really is the easiest and best way.
As for what acid to use, swim used to use gar but now used citric acid cuz he doesn't have to huff gar fumes that way (gar is bad for the lungs).
Swim's last rue extraction used 100g of citric acid for each round on a kilo. Probly overkill but it worked GREAT, swim got super yields doing it that way (Over 50g from his first two rounds, and there's still more in there waiting for him to quit being lazy!). There was no problem when doing the salt precip, apparently the 'loids turn into hcl salts and precipitate in the presence of NaCl regardless of whether they were cooked out of the seeds as acetate salts or citrate salts.
There is absolutely no need to use lye with rue. You don't want any NaOH ending up in your final product, there's simply no reason to risk it. Sodium carbonate is the perfect base for rue. Swim used to use ammonia but has given that up since he found sodium carbonate, it's perfect for this.
Finally, there is no worry about using distilled to clean your freebase. Last time swim had some freebase that he had already cleaned twice by putting it in near-boiling water, and when he went to clean it a third time he weighed it first. It weighed out at 50g. Then he boiled some distilled h2o, killed the heat, tossed in his alkaloids, stirred, and filtered. When weighed again he still had 48g, overall he lost less than two g of weight, some of which was not alkaloids but rather impurities.
Swim has recently found a brand of drinking water called Evamor that is ph9. From now on he plans on using this to clean his alkaloids. But distilled works fine, he knows this from much experience.
The ideal tek for getting harmaloids is as follows:
1. Boil seeds in citric acid solution, reduce to simmer, simmer for ~45min.
2. Strain.
3. Add 100g NaCl per litre of solution. Add directly to solution, heating if necessary to help it dissolve.
4. Refridgerate overnight
5. Pour off liquid from the top (you can save it if you wanna get the other alkaloids out by precipping with sodium carbonate, but be careful with these as they are somewhat toxic. Do not give them to pregnant women unless they want an abortion as they are uterotonic). Filter mush (by the way, I really like the syringe idea! BRILLIANT!)
6. Redissolve the mush in boiling distilled water. Alkaloids are already in salt form so no need to use an acid for this. Filter to remove any insoluble crud. Cotton balls work well for this stage of filtration, much quicker than paper filtering.
7. Use saturated sodium carbonate solution to precip fb alkaloids. Add until color stabilizes, then add a little more for good measure.
8. Pour off liquid from the top, and filter.
9. Bring distilled water, or better yet Evamor, to a boil. Kill the heat and let it cool just a little, then toss in your alkaloids. Stir briefly and filter.
10. Repeat step 9 until your wash water is clear to your satisfaction.
11. Enjoy!
Also, if you wanna separate harmine and harmaline, there is no need to use any nasty solvents as burnt suggested. One need only basify to roughly ph8, and the harmine will precip while the harmaline stays dissolved. One tek calls for adding ammonia dropwise to reach the desired pH, but sodium carbonate solution should work just as well with less stinkiness. Then after filtering out the harmine, basify the rest of the way to get harmaline.
That's really all there is to it. No need for any solvents, lye, alcohols... all you need is citric acid and sodium carbonate. It's that simple.
Much Love,
SyZ