Personally i have used ammonia 10%,can be found in pharmacies and its pure ammonia if you keep your eyes peeled for ammonia wityh no extra ingredients. Due to the amount of precipitation i used lots of it , basically i used it to redissolve the precipitant (in the hundrends of mls). Looks like it has worked so far. I chose it mostly because it evaporates clean so less contaminants in the final product (well, trying to minimise even minimal sodium carbonate one would have with the other base).
FOr Skullhuman: the basing , either way, will make alkaloids precipitate in freebase form whereas the water will still hold in solution previous contaminants like salt used in manske.
By the way skullhuman what quantities of rue did you use?
An idea: Is freebase soluble in alcohol? If it isnt then one could dissolve the manske precipitate int alcohol (does NOT dissolve salts like NaCl), filter the insolubles out, basify the alcohol and that should precipitate the harmalas. I wonder if alcohol can pull out different impurities that water can pull and if it would make a difference.