For the Mythos part, you might consider simply adding a Mythos skill as a workaround, rather than trying to force it into the Knowledge mechanic. You could also post a new thread here with "BUG:" in the title to let the Lone Wolf folks know about that particular issue. It might get lost in this thread so they may not see it. Plus they could let us know if it's not actually a bug but just some mechanic we're missing that way, i would guess.
The Skill die or d4 thing I had to do 2 Hindrances to cover it. It seems the most common method used in Hero Lab for a lot of that kind of stuff (think Half-Elves where you have 2 versions, one with Agility and one with a Free Edge.) The idea with using the Hindrance to bootstrap the skill bonus, though, is so you can not worry about placing that mechanic on the book it all (since the book makes it only temporary while you have it). In that sense having the sanity loss in the Hindrance is just fine as well because curing it is likely just going to be a Permanent modifier to the derived trait that you add in anyway. So I'd leave all of those mechanics in the Hindrance rather than on the tomes and then maybe put a note in the tome descriptions about adding the Hindrance.
So, yes, I agree that sanity and the knowledge/skill/hidden-AB gain should be in a Hindrance and the spells themselves linked to the book.
The Skill die or d4 thing I had to do 2 Hindrances to cover it. It seems the most common method used in Hero Lab for a lot of that kind of stuff (think Half-Elves where you have 2 versions, one with Agility and one with a Free Edge.) The idea with using the Hindrance to bootstrap the skill bonus, though, is so you can not worry about placing that mechanic on the book it all (since the book makes it only temporary while you have it). In that sense having the sanity loss in the Hindrance is just fine as well because curing it is likely just going to be a Permanent modifier to the derived trait that you add in anyway. So I'd leave all of those mechanics in the Hindrance rather than on the tomes and then maybe put a note in the tome descriptions about adding the Hindrance.
So, yes, I agree that sanity and the knowledge/skill/hidden-AB gain should be in a Hindrance and the spells themselves linked to the book.