Funny... just yesterday, I took another crack at getting it to work, hoping to post a success story.
As a bit of background, all this modding requires that I modify existing jobs or skillset indexes, since I can't ADD anything to the game data itself. Luckily the game has a ton of unused job slots, enough that I could make tons of custom classes, or unlock all the Guest-only classes for regular character use. After some fiddling around, I got a Red Mage job to work just fine... I created a new job over an unused index that learns a bit of Black and White magic, and can equip some heavier weapons. I've got Blue Mages working as well (though there are some animation glitches that still need ironing out), and they can use monster skills and even learn them on being hit by the skill.
However, for a reason I still can't figure out, all Blue Mages, both old characters that existed before I started modding, and recruits fresh from the guild, start with a random assortment of Monster Lore already learned. I know recruits sometimes start with random cheap Squire skills, so I bumped JP cost for each up to 9999, and even turned off the ability to learn the skills by JP. Characters are still starting with random Monster Lore though.
In my last test, I recreated the entire Job in a new index, in case the one I'd picked for Blue Mages was being used for some other game purpose. Even when I overwrote a Guest character's skillset, which I knew wouldn't cause a data conflict, and linked that to the custom class instead, the same thing happened. It might be something innate with Monster Skills, since monsters always start with them pre-learned... but if so, why do characters seem to learn from 4 to 8 Monster Lore skills, and more or less at random?
This is continuing to be difficult. :I