Thanks, actually i think that there like 5 places where you can raise your spirit, but i not sure, blue room at temple, maybe vivian, boss in tower, maybe church, aaaand, oh! Items, some items from shop actually raise up your spirit, pretty ironical how i said it, but yes, i think that it is all of them, if we wont count just level ups
So, notably this isn't possible on hard mode (you can't go over 3 starting spirit) and can only be taken once from Sophia. There's also the runes, as you mentioned, Vili's Wisdom perk, the teachers pet perk, three levels of "spiritual reserves" perk from levelup, and the nymph's blessing. Most of these (Vili, Sophia, and Teachers Pet) all have negatives, but are fairly easy to mitigate.