You are definitely missing more intelligence gains than you think. Crafting is based on intelligence and both of those items are crafted into other things at The Pounding Anvil. Also intelligence losses in the intro don't actually count; after you do the Bleak Tale, your intelligence and corruption are reset and then you are awarded some based on how much stuff you explored/interacted with in the intro, whatever the results may have been.
I mean, I know there were more of them. Those were just a few examples. I've also read every book in the Hoodton library, the dude with the potion in the Hoodton tavern, the drinking contest, and otherwise talked to every NPC I can think of, including but not limited to: Restoring Canisian forest, learning Stomachcutter, resealing the unstable portal, etc. There's only one event missing in the recollection room. There are only a few events I have encountered that I couldn't fulfill
Tried the Anvil and I got something like five items out of it, so that works. Everything but Bloody Cloth, so that's promising. Tried interacting with the bookshelves in the Crucible, still nothing for intelligence.
Edit: This may be just on my end, since I'm still running 4.3, and 4.4 is apparently out.
Edit 2: But I didn't get very far in the intro without getting saved by Hood, so maybe that's it.
Edit 3: Added a picture of the Int/Corruption Bars. Very little Int left to fill.