Let me start to dispel some of the mysteries here as best I can

. I like your observations, your picking up on some neat things here.
1) The reason why your solution did not freeze is because of a colligitive property(physical property) called freeing point depression. The more ions in solution the lower the freezing point of the solution becomes.

This is why if you put salt into ice water, the ice melts(and the water actually get's colder then 0*C/32*F).
2)Now why was some of the precipitate clear. It's salt(NaCl)! It came out of solution because the as the temperature goes down the solubility for salt in water decreases. Or perhaps you poured in a little too much, no big deal.
Now to the meat of it here, what your probably actually wondering about.
Well what the manske does is it forms the hydrochloride salts of the harmalas, ex: Harmine HCl, Harmaline HCl. Keeping in mind Harmala 'salts' are soluble in clean water. So before you added your acid, you already had them in their salt form. So what essentially happened here, this is my guess. You had an excess of salt in your precipitate(#2). Now there is an effect and this is actually how the manske works, when you have a 'salt' of an alkaloid(Harmine HCl) and you put it into a solution with a 'common-ion' in this case Na Cl(Notice the chlorides) the Harmala HCl's become less soluble in solution.
Back to #2, when you raise the heat of the solution the solubility increases(in this case). So your harmalas went into solution in the warm water. Then you added I'm going to assume here acetic acid(vinegar) which was probably room temperature. This cooled the solution, lowering the solubilities of the Harmala HCl's and the common ion(Cl- Chloride's). So I'm going to go on a limb here and say your precipitate is Harmala HCl's, these are generally yellow when fairly pure and brown/yellow when impure.
Now -
What you can do to receive the freebases is add NaOH solution to your acidified solution with some stirring.It won't be instantaneous and it may take a little more NaOH then you were expecting to use, but given enough time with the right amount of base you should end up with a tan to brown precipitate(dependent on purity).
Hopefully this helps!