Sure I can try to explain better.
1. Make your changes under a "Domain of the Faithful" (place holder, free to pick as you want)
-Why? This leaves the rest of the clerics intact so your changes only impact the subclass and another cleric at the same table can play normally without any conflict as a result your homebrew can be more widely excepted as an optional addition instead of risking being seen as an invader. Sure, you can have two characters playing at the table with different rules or maybe only one cleric and no issue but I think in general you will get less push back.
2. Like the totem barbarian sub class list all the domains and give each a minor and major ability. When a player chooses the "Domain of the Faithful" they select any deity and can choose ether to take 2 related minor domain abilities or one Related Major domain ability which will continue consistently down the "Domain of the Faithful".
Example: If the pick Thor they can chose the "Domain of the Faithful" major feature of Tempest ... or ... "Domain of the Faithful" major feature of War ... or "Domain of the Faithful" minor features of Tempest War.
- Why? This allows a unique blend and more accurate "portrait" of each deity because the followers of the deity can respect one side and not the other or both. Also, it allows you to make micro adjustment to each domain type similar to how warlock patrons very but its way more open to deity choices because you are not tying the abilities to the deity but to a specific deity but the domains the deity allows so any new deity, player made or Wizards of the cost made will automatically work unless they add a new domain. Then you just add one major and one minor ability option for that new domain and your cover all new deities that use it.
3. Add "Path of the mystic" and "Path of the Crusader" as class choices at level 3 the way warlocks add Pact of the Blade, Pact of the Chain, and Pact of the Tome to define how you play the class.
- Why? This allows variation in Mystic and Crusader under the same patron the way you wanted and you can fix one Path without breaking the other.
Example: (I am just going to brought from the book, I recommend you make your own taking the idea of the abilities instead of directly copying them)
Edit, I did make up Channel Divinity: Destructive Strike just mixing the name of the channel Divinities as a stand in for a Mystic specific ability
Player choices Cleric "Domain of the Faithful" --> Thor --> Tempest Major (Tempest spells & Wrath of the Storm) --> Mystic (Channel Divinity: Destructive Strike)
Player choices Cleric "Domain of the Faithful" --> Thor --> Tempest Major (Tempest spells & Wrath of the Storm) --> Crusader (proficiency with martial weapons and heavy armor)
Player choices Cleric "Domain of the Faithful" --> Thor --> War Major (War spells & War Prist) --> Mystic (Channel Divinity: Destructive Strike)
Player choices Cleric "Domain of the Faithful" --> Thor --> War Major (War spells & War Prist) --> Crusader (proficiency with martial weapons and heavy armor)
Player choices Cleric "Domain of the Faithful" --> Thor --> Tempest Minor & War Minor (Tempest spells & War spells) --> Mystic (Channel Divinity: Destructive Strike)
Player choices Cleric "Domain of the Faithful" --> Thor --> Tempest Minor & War Minor (Tempest spells & War spells) --> Crusader (proficiency with martial weapons and heavy armor)
Any way you would need to figure out what you want for the major and for the minor abilities, I actually use them like two minor abilities above to show scale and that would work too but you could make more powerful single abilities for the solo domains and weaker abilities that reflect the same intent for the combination of 2 domains. I think there are 13 domains so you make/alter 13 major and 13 minor and you should be able to accommodate any deity.
I hope this clears up the the thought process for you. Best of luck.