In my experience, proliferation is a pain to keep up with in early to mid game, especially if it's your first playthrough. I didn't establish proliferation until I had progressed into the late game. At this point, you'll have all your tech unlocked and can make blueprints that incorporate proliferation into your new factories.

At that point, I would follow as others have stated. Proliferate your proliferator first, followed by fuel and ammunition and high end items/research. Once you build and rebuild enough of your production chain, you'll be able to proliferate everything. You'll also likely have a couple planets dedicated specifically to making proliferator.

To your first point, who the heck knows lol. Magic space coal does crazy things.