I'm attempting a DHH->THH reduction for a second time. Since I have HCl now, I thought I'd dissolve my DHH freebase in that instead of vinegar.

I put 7g of DHH in a glass, added 200ml of water and around 10ml of 36-38% HCl.
It took a lot of stirring and heating to dissolve the harmalas, so I thought there wasn't enough HCl in it, but when I checked the pH using a pH pen, it turned out to be very acidic (pH 1.0). I thought it would be much higher as with vinegar. Also my teaspoon developed stains from just stirring the solution for a few seconds.

I'm assuming it's not a good thing for the pH to be that low: not good for the reduction, the subsequent basification and possibly for the alks themselves. Or is it ok?
Should I try to raise the pH somehow, or just let the HCl evaporate over time? How long does it take for it to evaporate and what pH should I aim for before adding the zinc? Once that pH is reached, should I still add vinegar, or will the HCl work as well as a reducing agent along with the zinc?

The problem was the solubility of DHH•HCl
Harmala hydrochlorides are poorly soluble in water and very poorly soluble in solutions of chlorides, including hydrogen chloride (HCl).
But if you have it in solution at room temperature, hydrochloric acid will react with zinc to reduce DHH to THH, it'll just go much faster than with vinegar. If you have a magnetic or mechanical stirring thing available thats no problem. Even without, it may not be much of a problem.
If your worried you can take some vinegar and add some baking soda (caution, foam) the sodium acetate thus formed will serve as a buffer to turn the hydrochloric acid into sodium chloride and vinegar.
If you see crystals form during reduction warm it up to dissolve the hydrochlorides, but dont warm it too much if theres still hydrochloric acid in there, the fumes are a bitch!

Thanks, I didn't know that. I thought my harmaline didn't all convert from freebase to harmaline HCl; now I understand it did convert, but much of it stayed as harmaline HCl crystals. And as the HCl gas evaporates and the pH of the solution rises, the harmaline HCl will become more soluble?

Presumably that's why it's recommended to use 50ml of 1% HCl for 1 gram of harmalas, rather than a smaller volume of more concentrated HCl (which is what I did, although it was still around 1.6%).

I do have a magnetic stirrer, and a heated one at that. The only thing I'm worried about is the potential consequences and risks of working with pH around 1.0.
Will wait a bit more and check the pH, if it's still that low I might do the vinegar and baking soda thing.

After the reduction is completed, based, washed and dried, I'll want to convert the freebase THH to THH HCl for long term storage. I'm assuming in this case there is no need to use low concentrations as I only care about converting and not dissolving. What concentration would you suggest? Can I just pour a few drops of the original 36-38% HCL over the THH freebase for the reaction to take place, and dry the crystals?

If the THH base does not fully dissolve before hydrochloride starts crystallizing then there would be the possibility of THH•HCl crystals encasing particles of THH base and preventing it from reacting and you'd have freebase contamination of your product.
Regardless if I used just THH and HCl or a manske-styled THH, vinegar, and salt method for making THH•HCl I would make sure it was a clear solution at some point before forming the hydrochloride crystals.

Your acid concentration probably isnt sufficient to cause any harm.
If harmaline is heated/boiled in 36% hydrochloric acid it is converted into harmalol, the same stuff our bodies initially make it into before glucuronidating it and peeing it out.
I wouldnt worry about damage done by luke warm 1 or 2 molar HCl.

If I use 1-2% HCl to convert fb to dissolved HCl salt, the large volume of the solution will leave me with a lot of evaporating to do. Somehow I thought the harmala fb -> harmala HCl conversion was easier and less energy/time consuming.

An update on the reduction:
I added a little bit of vinegar with sodium bicarbonate (just enough vinegar to dissolve all the sod bicarb, pH ~6.3) to the DHH HCl solution, which brought the solution from pH 1.0 to 1.3. Then I added zinc and put it on the magnetic stirrer without heat (T+0).
At T+1.5h the pH was up to 2.0.
At T+3h the pH was 4.5 and the liquid doesn't glow green in UV anymore, which indicates the reduction is complete
The constant stirring must have helped drive out the HCl gas.

Edit: I let it reduce for a few more hours for good measure. When I checked back, the pH was up to 6.5, the solution was green again and had a lot of freebase floating about.
I've now added vinegar to bring the pH back down and am going to leave it for a few hours to reduce again.