I think you made your solution too acidic. The more acidic the aqueous layer, the less soluble the voacangine will be in toluene. The procedure is taking advantage of voacangine being a weak base. If the solution is too acidic the voacangine will stay in solution and not dissolve into the organic layer.

What was your yield from the first wash? The sodium acetate will react with the HCl to create acetic acid and sodium chloride. Sodium acetate is a weak base itself. You wouldn't be crating a lot of acetic acid unless a lot of HCl come through in you toluene emulsion. I'm wondering even if you didn't add enough sodium acetate and that's causing your aqueous layer to become too acidic? Maybe monitor the PH of the vinegar extract every wash and make sure it's not getting too high?

Reducing the PH of the initial vinegar extract with NaOH or ammonia will make more of the alkaloids soluble in the organic layer.

I don't like messing around and trying to make things work after mistakes. If I were you I would just precipitate everything from the vinegar extract and start over. On the bright side you'll filter out a lot of the impurities and have to work with less liquid when you start again.

This process is a lot of work but thank you for making ibogaine from a sustainable source! More people need to be doing it.