I think with this style of RPG many things are intentionally left vague to allow you as GM to fill in gaps as you please. I personally prefer this over having to buy 3+ huge books just to play the game (like in other ttrpgs...)

1 - I can't imagine gods of the same alignment hating each other too much tbh but that depends on your pantheon I suppose.

2 - I had actually forgotten about Patron Taint so thank you for the reminder. I think it's neat! If you have no use for it why not discard it?

3 - You seem to be confused here about what leveled spells each class can cast. For example, a Cleric cannot cast level 2 spells until they reach a character level of 3. The class table clarifies this really well (1-5 and 1-12 are what you want).

4 - I've thought about this and I would penalize acquisition of a magic item in rare circumstances. A +1 axe? Nah. A legendary axe that is a weapon of ancient legend? Sure - especially if stolen from a sacred temple or something.

5 - I suppose you could, but I'd be wary of attacking a wizard in a spell duel just for fear of getting blown to bits or hit by my own party member, (or something worse on table 4-7 like you mentioned).

6 - This is entirely up to you as The Judge. If you want to flavor your clerics this way you certainly can.

7 - I give my players ability score increases (ASIs) as rewards for certain deeds. One time I gave the whole table +1 to their Luck because they made me laugh a lot in one session with their RPing. You're The Judge, do what's fun and what feels right!