I have some experience with Blender such that I can make a semitransparent cylinder of specified dimensions and small spheres. I want to (for a chemistry tutorial video explaining temperature and heat concepts) write a program that will:
In other words, by #4, this program doesn't even need to be GUI at all. I just want the program to make a video.
It may take me a very long time to actualize this because though I have a lot of experience with C, C++, and Java, I don't know how to take a 3D model file and programmatically control it. I don't even know the infrastructure of libraries and accompanying API to control 3D objects and record the camera to a file.
Are there any tutorials that would go from starting with some 3D models to programmatically setting up a scene (objects, camera, lights), programmatically moving the objects in the coordinate space, and recording the video to a file?
Knowing some programming already, I want to point you to Unity, www.unity3d.com
Unity is a 3d game engine, though it can be used for a number of different things, including this program you have in mind.
It's programmed with C# or Javascript, and I think you could pick these languages up easily enough.
Basically what you described in your last paragraph is exactly what Unity does.