Keep in mind that in Yasu's and The New Hope's church faith, there is no death:
A god being dead, especially the one she seems to follow would equate to a god being on a second plane of existence. Frankly, her story about the person who was born blind, sewn eyes to himself, then died and saw through the lives of others, seems to be the origin story of her god. This was mentioned in Yasu's 'Sakura Season' Event:
In other words, her god seems to have became a god after it died. Sensei's brother, Nozomu, dying, then HOPE showing up could be why they are equated. HOPE can also translate to Nozomu in japanese.
HOPE has also been mentioned to have many eyes:
Like Yasu's god:
Sensei and The Player can only apparently see two of those eyes.
John also seems to sound like HOPE:
So, if there is a ressurection going on, it'd probably involve HOPE when it comes to John.
Btw, Yasu loves the Summer:
But does not like the Winter:
Fun fact, if Yasu is wearing mostly black, it's probably Summer. If she's wearing mostly white, it's probably not.
Overall: It's very likely that the god called Nozomu, The Callous god, and HOPE, as well as Yasu's god are all the same thing.
Now, as for the confusing parts, I think you've conflated USER2 and USER3 with other things. USER3 is Pareidolia, The Concerned God, and The Dark. It usually talks in lower case. HOPE doesn't. HOPE has had seemingly nothing to do with USER3/Pareidolia so far.
It also probably wasn't USER2 who affected John. John was presumably talking about The World Itself, hence it mentioning "tendrils"
And Yasu seemed extremely scared of the tendrils of sky:
Which seem to come from The World Itself, as that was the thing Yasu was talking about at the time:
This might be the thing that scared John and made him incomprehensible. Albeit, the World Itself is somewhat of a mystery. It seems to be related to The Sky, and Sekai though. It also seems to be somewhat HOPE's opposite, if not perhaps it's Devil, but that's just a theory.
Overall: HOPE shouldn't be an emissary of Pareidolia/USER3, and USER2 probably didn't do anything to John. Yasu also loves the Summer. As for the Tree stuff, that seems to be USER2's thing, but all the gods have some relation to the tree:
And the universe itself is a forest: