I dissolved 5g harmaline in vinegar, then added some tap water, 5g metallic zinc (used previously and somewhat dirty and clumpy) and a bit of HCl. The pH went down to 1.8. Adding the HCl made it instantaneously turn yellow.

I kept it on constant stirring for 9 hours. When I turned off the stirring, it turned out to be very thick and took overnight to settle. A thick layer of yellow precipitate has formed, as thick as the aqueous layer.

Does anyone have an idea of what the precipitate could be, and how I can recover my alks?

I decanted the supernatant and based it, and very little precipitated from that. So I concluded that most of the alks must have been trapped in the acidic precipitate.

The acidic precipitate dissolved in hot water, which led me to believe it was harmaline HCl, which was created when HCl got in contact with harmaline acetate. I didn't know the HCl would displace the acetate ion like that. It hadn't happened to me before. Maybe it only happens in high concentrations of HCl.

A bioassay showed that it was still mostly harmaline and very little (if any) THH. I'm going to have to repeat the reduction, this time I won't use HCl.

You rediscovered the manske chloride precip, this time using hydrogen chloride instead of sodium chloride. Same functional principal either way.

In that case, using HCl may be preferable to NaCl. It avoids heating / cooling, salt contamination and salt pollution of the environment. Just add a bit of HCl, wait a few minutes for the precipitate to settle and collect it. The only catch is you have to wear eye protection and gloves, and HCl is less OTC. Is it really that simple?

Yes, you can do that. I saw an old school published chemistry paper that used conc. HCl to crystallize harmalas once but as with NaCl you need to pass a certain threshold concentration for it to crash out the vast majority of harmalas otherwise you get something proportionately between harmala hydrochlorides low solubility and manske-style near-insolubility.
And, really, I'd rather make a mess with salt than make a mess with concentrated hydrochloric acid- the stuff just isnt friendly.

this ^ +
mildly put, it's seriously corrosive, even as vapors.
playing with it in your living space would be just plain dumb.

Yes I tried crystallizing harmala hydrochlorides from plain water, but the yields are low even if the solution is cooled. The salt really helps push things out of solution.

The yellow is probably harmaline crashing from solution.