Some answers to your questions:
1. As a new ressource to create stuff, but mostly unused right now
2. Yeah, noticed stuff like this, too. Also generally play at fast speeds since there's not too much to do (on a sidenote, I do the same in Prison Architect all the time)
4. Miners not mining anymore: Every resource has a (hidden) maximum amount that's allowed in storage. From your screenshot it looks like your storage is pretty much overflowing of rocks. So you need to get some of the rocks transformed into blocks to get the miners working again. And your problem under number 3 is probably linked to this, too.
6. Either 6x6 or 7x7, but I personally don't press my luck and put pillars whenever I hit 5 large.
7. Will certainly come later, but right now, it seems to be the only way.
8. With the Earthworks you can transform wooden logs (32 of them) into coke fuel. (Only) useful if you got plenty of trees but no coal vein nearby.
9. Planned for later as far as I know, but that has't been programmed yet
Oh, and fishing rods can't be used yet, just as there's no hops yet to plant even though the option for the fields show up