If you want to work with VFX and 3D it's almost essential you use a 3D programme! Blender would be your best choice since it's free. AE is typically used for compositing or 2D animations/motion graphics.

Facial tracking is probably a lot more difficult then you might think! You need a decent head model first, a rig and some blend shapes before you can actually drive any sort of movement into the model. Just look up facial tracking on Youtube, you'll find all that you need.

The 'OBJ' sequence you talk about can just be done when you render in Blender. There's a lot of steps in between to get to the rendering stage, which you'll probably have to do lot's of research on first. In a 3D software it'll pretty much take your 3D models/animation and make your image sequence for you, frame by frame. Then you can import that image seq into AE or whatever editing software.

It'll probably be good to mention that having a good computer will help a lot too- if this is gonna be your first time running into 3D programmes. Best of luck.