Thank you for this insightful and honest account of your experiences.
As a coach, I have witnessed that the complexity of complete self-organization leaves many well-meaning companies overwhelmed and stranded. I do subscribe to mindsets that are in synch with many ideas brought forward by holocracy and recently published an article on Medium in which I speak about these mindsets and their application (“What The Patreon-Crowdfunding-Model Teaches Us About Leadership”). I support organizations to transition to more creative organizational structures and tend to do it in a more gradual fashion that takes into account that less external structure requires more personal self-awareness by all individuals involved, in order to work. The evolution of the individual and the collective consciousness have to go hand in hand.
Also I find that one of the main principles that is not considered amongst self-organization disciples is that of Source (see: Who’s Idea Was It Anyway?). It does make a difference what one person sees as the future for the organization they founded.
I think it makes sense to have the transition be a slow and evolutionary “trial and error” process in which you figure out together how much or how little is the right amount for each company, and each founder, their vision and their team. Sounds to me like you are on the right track.