Thanks Jees and pitubo. Now this is confirmed, an older document from Phlux also confirms this as he merely neutralized the solution and already got "almost pure harmine", filtered and only then proceeded with further separation.

I will try it again with ultra pure free base harmalas, dissolve in dilute HCl and titrate with dillute ammonia and see.

Keeping the solution at low concentration (excess volume) might help too.

Sorry, OP for stealing the thread for this discussion.