Hey OneWolfe, thanks for the reply!
Yeah I think I opened one of the pottery pots before picking up the rest of them, which must have changed its metadata. Anyway, the names of the other two buggy quests I couldn't complete were "Think Nickel Plating" and "Silver Fauxe Fur" in chapter 7. Once again, I think it's a metadata issue. I had the rods collect silver / nickel, but I guess since they take damage in the process, and/or they can have a variable amount of flakes on them, the book doesn't recognize them?
Also, the inability to make wooden cogs blocks the whole chapter 3 questline, that's probably a pretty major problem.
Clockwork Engines huh? Hmm that sounds doable. Is there a reliable way to get slimeballs though? I haven't seen any slimes yet and I'm in year 3. I just have a couple slimeballs in storage which I think I got from reward bags or quest rewards or something.
@ColdComfort, I play SSP and I haven't really had much of a problem. I ran away to a small island to escape the onslaught for the first few night or two. Most of the enemies seem to despawn when the sun comes up. Whatever remains can easily be taken care of using several stone axes. But if you run into those ridiculous pincer beetles or annoying mountain trolls you better turn tail and run. I think the biggest advice I can give is to live near a coast, or better, on a small island off the coast. After a couple days spawn protection will kick in, and hostile mobs won't even spawn anymore.
If you desperately need a wall, you can use dirt/sand/gravel for the first layer, and put log piles (with a single log in each) on the second layers. That way you can easily remove the logs by hand later. Or well, you could use cobblestone walls like the questbook suggests. (I didn't realize I could make them with just 6 stones, I was looking at the vanilla recipe which requires 6 cobblestone so I didn't use them for a really long time). Either way I haven't really needed to wall in though.
On starving: I had serious hunger problems especially since I couldn't find any crops for the first few weeks. Luckily you don't actually die when you run out of hunger. After running around with an empty stomach for a day or so, I noticed I could eat seaweed, so that's pretty much what I ate for the next couple weeks until I found other food sources.
Edit: Ahh, you are trying to use javelins. That explains why you're having so much trouble, lol. Javelins are worthless, don't even bother with them. Just make a bunch of stone axes and whack them in the face! You could make a couple walls or fences at your house entrance to make it easier to kill the enemies safely rather than fighting them at your door.
As for the food suggestion, perhaps some early quest rewards could also be saplings for things that you need for later quests? Like, a red apple sapling, and a chestnut sapling would be really useful. I got a bunch of willow saplings from reward bags, dunno if I was lucky.
Or perhaps the reward bags could drop small quantities of common vegetables or something. That would support the early game hunter/gatherer lifestyle.
And feel free to look into how the Zombie Awareness mod works, there may even be some clues for how to take advantage of the mob AIs.