Is each spell linked to only one rune?
So an initiate would need skill in at least four runes to cast rune magic; magic, spirit, truth and other rune(s) for cult specific spells?
If a spell is linked to multiple runes which rune skill would be used to cast it? Players choice?
I think I prefer it simpler if that initiates, priests and lords use their own runes. This would mean that someone with a fire rune, because they are a Lobril worshipper, might use other fire magic in the course of a scenario (perhaps a fire related magic item), but trying to use e.g. darkness magic, would be impossible.
Apologies if I have misunderstood your meaning.