-_- soooo many questions, all of them really good. Try to answer as best I can...

As for how he stores the souls, he stores them inside an organ that's attached to the stomach. It's sorta like how a cow has four stomachs. Only one processes food, while the other processes souls.

As for the souls in question it's magical, and scientific. It's magical in the way he litteraly drains the life force from them. Then his organ processes it into a usable energy which powers everything which is a scientific process.

Now for the portals, the scythe Grim has causes a tears a tiny hole where two dimensions join. In a way it's like nightcrawlers ability to pass through one dimension to end up where he wants. Only it's far more stable due to the fact he understands it on a scientific level.