I did another experiment: after several A/B (vinegar/NaOH) and two makes, I had yellow clean looking HCl salts. I dissolved them in water and based carefully with ammonia drops and a pH meter, stopping after the second pH drop/rise depression, when harmaline finishes crashing per the VDS protocol. 

After separating out the harmalas with a filter as usual, I added NaOH to the filtered liquid. White stuff crashed. It dried to flakes (see image). Harmalas dry to a crust that becomes a powder when crushed, this seems different and more flaky. It is a small amount (650mg), about 10% of the bulk harmala weight, but is did survive all the other cleanups.

So stoping the pH rise once harmaline precipitation is complete may be useful as a cleaning step (compared to bombing with NaOH). Harmaline precipitation can finish at a pH as low as 8.5 per the VDS protocol.

I wonder if when acidifying to dissolve the FB as a salt there is a similar situation. Perhaps lowering the pH below 3 helps dissolve unwanted stuff. Maybe tracking the pH as vinegar is added to water and the harmalas go into solution could be used as an indicator. Perhaps at pH 5 harmaline and harmine are both in solution and more contaminants can be separated by stopping at a milder pH.

In short, there could be a smaller pH range that still yields well and at the same time helps keep contaminants out.