Alright, I've managed to implement everything that you have pointed out so far Exovi except for Venom Might not working. Thanks for your contributions. I can tell you seriously scanned these files! :O
For Venom Might, it seems that the skill or required-skill sections are stopping the passive damage bonuses from working, because as soon as I remove them, the damage scaling works immediately.
This is a interesting problem I'll have to investigate very in depth on the weekend because the skill/required-skill fields are used to scale mana cost (at least I think). So, I'm not sure what I can remove safely versus not. And, in fact, I may need to use a different system for poison that I am now remembering (which is why I didn't implement Venom Might with the other mights I'm realizing).. but that'll be a ways off in any case if I decide to do that system....
In the worst case, I can just implement venom might as a permanent status effect buff. But, I will try to avoid that and use the most simple, intuitive and cohesive solution once I figure it out.
Also, for spells, my most recent solution flopped, so I still think the current 'might' system is about as good of a system as I can get. I really can't do much more than that. :*( In any case, I'm compensating Mage's with double base spell damage in the next patch. Yay!
So, the current plan is to fix this venom might scaling in depth and then I'll shoot out the next patch (probably Friday night). Also, I'm really confused why so many spells are not included in my skills file. I know I siphoned a bunch out to put into my separate files, but I'm surprised by how many wound up missing. I think I might have copy-pasted skills into a file that was overwritten at some point, which would explain why random skills are gone (like poison arrow isn't in any file atm, which is fine because it's a status effect, so maybe it was intentional... but still).