Until JSF 2.3 the mojarra (reference implementation) and myfaces were based on JSR specification document.
With a move to the EE4J:
Update August 19, 2018: Guillermo González de Agüero recently gave an interview at Jaxenter.com addressing some of your questions. In particular, he's a bit worried that Oracle won't open-source the specification documents. That'd prevent simply taking these documents as a basis for new specification documents.
Update August 17, 2018: After writing my initial answer, I reached out to some of the leading JSF developers (see this discussion on Twitter). There are plans to purge outdated APIs, such as removing the old JSF ManagedBeans in favor of CDI. So there will be API changes, but I don't thinks that's something to worry about. I'm sure there will be a smooth upgrade path.
It's always difficult to make a prediction concerning the future. However, I'm a bit closer to the people in the spec teams than most, so I can make some educated guesses.
EE4J is part of the Eclipse foundation ecosystem, so I'm sure there will be a well-defined specification process and a lot of documentation. I'm almost sure there will be a detailed specification document, but take it with a grain of salt - I'm not an insider. (Also see update above - currently, the specification documents of JavaEE are under copyright protection, and it seems unlikely they're going to be donated to the Eclipse foundation).
As far as I can see, there's not much impact on MyFaces. They just have to follow a different specification document.
Definitely yes. MyFaces is an actively developed project meant to be a plugin replacement of Mojarra. That won't change just because the reference implementation went from a big company to the Eclipse foundation.
There won't be much of an impact to PrimeFaces and BootsFaces. Both projects will remain compatible to both Mojarra and MyFaces, and to every current version of JSF. There are other JSF libraries such as HighFaces which rely on internal API of Mojarra. But even in this case, there won't be much of a change.
In any case, I don't expect major breaking changes of the JSF API in the near future (apart from purging outdated APIs, such as dropping support of ´ManagedBean`). The strength of the Java world has always been backward compatibility. But again, that's just an educated guess, so take it with a grain of salt.