A few things scream out at me immediately, a standardised education for all, if a school exists, a madrassa, there must be one standard, that MUST comply to standards.
The must be a way devised to separate the clergy from politics and role in state affairs, to get religious tolerance, you need to make religion a personal thing, not for all to wave around and in other people's faces.
Go to any religiously tolerant country, they do not like discussing religion, they explicitly avoid religious discussion in most of their affairs and especially in their professional life and work.
Politicizing anything, and you'll get the worst out of it and possibly the best, but the worst is always the cause for concern.
Also a standardized body for religious teaching, not to own it or dictate like the Historical example of the Church of England, but a body to regulate.
Social change on it's own looks difficult if the foundations are missing.
The above might lay the way for future generations to be more accepting of each other.
And the right kind of it.