It sounds like at least part of your problem is related to circular dependencies. Aside from this, unfortunately, blueprints have numerous hard to replicate issues ESPECIALLY when projects reach a certain size and complexity. I know they are actively working to resolve these issues, but it will take time. You can contact epic, about this by posting to answerhub.
In the interrim, this thread:
Lastly, another solution is to move your boilerplate functionality to C++ (which is what we did for our project - we were going to do that anyway, but we just had to do it sooner rather than later)
-fisj