I might derail the thread, so ignore my answer if it is not what you are looking for....
You are talking about creating a large world. Yet on the other hand you seem to struggle on some pretty low level stuff (no offense meant, really)...
On the other hand you seem to have a pretty concrete project in mind.
Thus my question: what is important to you, getting ahead with that project of yours, or learnong how to do these kind of things on your own, the low level way? Do you want to create a game, or do you want to learn how to low level plumb an engine so it could cope with a larger world?
In the first case, think about starting to use a game engine to get away from re-inventing the wheels here, and get into creating your game/world faster. While it is certainly a good learning exercise to be able to do everything yourself, it is extremly inefficient for any larger/more complex project (don't know how complex yours is, really).
That is why almost none of the big studios nowadays creates an new engine for a new game, and why most actually buy an engine to build their game upon.
Question one you have up there would be already solved by the engine for 99% of use cases... you might still have a special case (needing to load millions of objects fast, or something like that), but then you would still have a better chance to solve this problem in an existing engine (Either by issuing a feature request, or by modifying the engine code, if available).
The second question is also already solved in most engines as others have done this before. Most engines come actually with tools for creating cutscenes nowadays, which seems exactly what you want to do there.
If you are interested in a 3D Engine, I would recommend Unity 5 or Unreal Engine 4. IMO Unity is a little better for a beginner, and Unreal Engine gives you more options and power at the high end. Both have large communities and documentations, and are pretty up to date.
Of course, if you are trying to learn the low level plumbing, nothing beats the DIY approach. In this case, please disregard my comment.