Good points there!
1. I think you're right on this and I'll double coal usage, see how that goes.
2. That's by design, although not a good or at all clear design :) There's a hidden number for an amount of each type of item to produce. Stone blocks is 300 and there's something similar for planks and metal. This is a placeholder until the player can specify what should be produced, which is scheduled in for Alpha 4.
3. This sounds like a bug that I thought I'd fixed, twice! Although they are meant to pick the nearest point in the river (if there's no closer barrels available) as the crow flies, which can end up being a poor route if there's not a direct path. I'm adding something to make it clearer if water barrels are available or not. If they seem like they're going clear across the map to the river and not picking anywhere at all near, I'm looking for a save file to investigate this.
4. This is also by design, as they do produce some mushroom spawn when complete, but only enough to start another single mushroom log. The intention is that you'll only be able to have as many mushroom logs as mushroom spawn that you find in the caverns, instead of doubling it every time like the outdoor crops. If that's a good idea or not I haven't decided yet.
5. Hops and barley are implemented in terms of the crops and what they produce, but until brewing beer is implemented they don't have a use, so I've removed them from being included on game start to avoid confusion - and also so you don't randomly start with lots of hops and barley and little edible crops and starve. When they're back in (also aiming at alpha 4) there'll have to be something to balance the starting seeds.
6. This was a bug, there was meant to be a hidden value to create another anvil when the first is used (see point 2) but it was missed out of the current release. It's fixed in the next release which I was intending to have out now (just one more thing to add) but unfortunately it'll only apply to new games due to the way the crafting system works. Again, it's due to be replaced by a screen the player can use to manage crafting/production.
7. There's quite a few other ore types already, with more to come, though they spawn in different "groups" of rock (sedimentary/igneous/metamorphic) which you only tend to find inside the mountain compared to on the outside, though there's no guarantees with the map generator. While there's no real difference between different metals right now, the intention is they'll have different properties/hardness/value, so things like gold are found deeper in the mountain. There's tin too, though that might be it for now? Alloys and steel are on the roadmap but not implemented yet.