Alright, so currently you want Heroes, Mythos, and Spirits to have skills points correct? Is there a reason why Servitors would not have a skill?
Before you assign numbers, you might want to consider the ratio of strength between each category and then base the numbers upon that. How strong do you want Heroes and Mythos to be compared to each rank of Spirit? (You've mentioned a couple times that you want mythos to be able to challenge Spirits, but in general, I do not think that most of the current mythos that have been made actually pose a threat to Spirits. Dragons and Kraken possibly, but they are a minority. I suppose there could be special cases of mythos that are that strong if they are given the correct abilities under the new definition.)
How many sources do you want to have applied to the potency of each skill? Seems like you have quite a lot at the moment and possibly cutting some out could reduce having the really large numbers.
The main problem I see is that you're creating a system that promotes Pantheon leaders with crazy high skill scores and that was one of your main complaints in the First Age (Smites x6 and Pantheon Leaders solving all problems with no effort).
Romans 8:31 What, then, shall we say in response to this? If God is for us, who can be against us?
1 Corinthians 13:1-3 If I speak in the tongues of men or of angels, but do not have love, I am only a resounding gong or a clanging cymbal. If I have the gift of prophecy and can fathom all mysteries and all knowledge, and if I have a faith that can move mountains, but do not have love, I am nothing. If I give all I possess to the poor and give over my body to hardship that I may boast, but do not have love, I gain nothing.