Pretty good mod so far, although the different patrons feel a bit samey after a while, but it adds a little flavour to the game. I have a few suggestions for Islam and Judaism.
For Sunni Islam, instead of a patron saint, Sunni leaders should be able to adopt one of the four main schools of Sunni jurisprudence: Hanafi, Shafi'i, Maliki and Hanbali (there are other schools which are now extinct, but which may have been available back then). The option to choose a school of jurisprudence should be open to all leaders, Court Imams, anyone with the Chief Qaddi title or anyone with the Faqih trait. If a ruler and his Court Imam or Chief Qaddi choose different schools of jurisprudence then they suffer mutual negative opinion, as well as certain events showing the negative effects of conflicting legal practices (if all three take different schools then hilarity ensues). If they choose the same schools then they get opinion bonuses and positive events showing an effective legal system.
It should be noted that the Ibadi sect of Islam has its own particular branch of jurisprudence, so it wouldn't make sense for them to have a choice.
For Shia Islam the ruler can choose to emulate and revere a particular Imam, figures who are regarded as having a particular religious and moral authority, as well as semi-divine qualities and infallibility (but they are definitely not prophets). Just which Imams are available would be somewhat contentious. Modern day Shia Islam is divided into three main groups: Athnā‘ashariyyah (Twelver), Ismalis (Sevener) and Zaidis (Fiver), who revere 12, 7 and 5 Imams respectively. I'm not entirely sure of the history, or how appropriate it is to revere a particular Imam, but it may provide a useful parallel to patron saints. Alternatively a similar system of jurisprudence based on Shia schools could be implemented.
For the Yazidis have the six other angels beside Melek Taus, but I don't know enough about them, nor can I seem to find much information about them.
For Judaism there isn't any initial parallel to patron deities, but there could be a possibility to revive the old second temple era sects, if the third temple is rebuilt. There were four main sects at the time: the Pharisees who were the party of the rabbis and the precursor to modern rabbinic Judaism and quite popular among the common people, the Sadducees who were the party of the priests who had their main support among the upper classes, the Essenes who were an ascetic, communalistic sect, who believed in non-violence, vegetarianism and with some groups practicing celibacy (there are parallels that have been drawn to monks), and the Zealots (no prizes for guessing what they were like), who it is already established get revived once the temple is rebuilt. In addition there were also the Sicarii (Siqariqim in Hebrew), an even more violent and fundamentalist offshoot of the Zealots who performed assassinations and terrorist attacks.
The way I think it should work is like this; 10 years after the rebuilding of the temple you should get a message that reads:
"The old ways are being restored and with them old antagonisms are returning. Conflicting interests between the Rabbis and the Priesthood has led to a revival of the Pharisee and Sadducee factions of old. The Zealots continue to grow in popularity and are rapidly becoming a mainstream presence in [kingdom name] politics, much to the chagrin of both the Rabbis and the Priesthood. Even within the ranks of the Zealots, however, there are disagreements. A small sect of fanatics, claiming that the Zealots don't do enough to punish the enemies of the Jewish people, has broken off. Styling themselves after the dagger-men, or Siqariqim, these fanatics have sworn an oath to hunt down all who they see as enemies of the Jewish people. The recent discovery of an ancient cache of religious texts in a cave near the dead sea has revived interest in the ancient sect of the Essenes, whose docrines of non-violence and communal living have already began to attract a following amongst those seeking to escape the hardship and conflicts of daily life. As [ruler title] your patronage of one of these groups could be very beneficial for you, but be weary of the political consequences of your choices, as not everyone will be pleased with who you choose."
After which you should then be able to pick a sect to back. The bonuses and drawbacks should work something like this:
Pharisees: positive temple vassal opinion, positive city vassal opinion, +2 learning, piety bonus, lower revolt risk, negative religious leader opinion, negative noble vassal opinion
Sadducees: positive religious leader opinion, positive noble vassal opinion, prestige bonus, +1 stewardship, +1 diplomacy, negative temple vassal opinion, negative city vassal opinion,
Zealots: +2 martial, -1 learning, -1 diplomacy, negative temple vassal opinion, negative religious leader opinion, can only be chosen if Zealous
Siqariqim: +2 intrigue, -1 learning, -1 diplomacy, negative temple vassal opinion, negative religious leader opinion, can only be chosen if Zealous
Essenes: +2 diplomacy, +1 learning, lower revolt risk, piety bonus, -2 martial, -1 stewardship, negative city vassal opinion, negative noble vassal opinion, negative religious leader opinion, negative temple vassal opinion, -50% fertility, cannot declare holy war, prestige penalty, cannot be chosen if Hedonist, Lustful, Greedy, Gluttonous or Drunkard