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Aegon's invasion is happening in the books. They take Griffin's Roost.

You are right! hehe Just checked it again and I was wrong.

At any rate, there's no telling if Danny's invasion happens too, most likely it does. My theorycraft about the books is that Varys basically plans to make a incestuous wedding between Aegon and Daenerys, so there's absolutely zero pretenders to the throne and it goes back to the Targaryens with Aegon in charge (but it's bound to fail, obviously)...

I've also noticed a massive spam of script errors when the Red Wedding happens, same goes if you actually go to the twins during it... Idk if it was to accomplish anything, but apparently nothing happens/changes if you go there and win or simply ignore the event all-together...

to me the weirdest things are that Joffrey stays alive, Daenerys' unmarriable, The Hound stays within Joffreys army, Jon Snow remains practically inactive within the Night's Watch while Bolton rules the North. Reek never appears, instead Theon's locked within Danny's Army, and the Aegon "invasion" feels cheesy considering we have no idea if it ever happens in the books.

So both "timeline" options are sort of incomplete. In fact we don't even know if Aegon's in fact a Targaryen or a Blackfyre

What are your domestic policies? If you have it set where sworn lords don't have as much power/autonomy they don't like it whereas if you give them more power you get small pluses once in awhile.

This (I'm sure) + Unassigned fiefs (not so sure)

Many of these effects come from Diplomacy mod, and within Diplomacy mod one had to be strategic as to how they managed their kingdom/lords. Given you have a source of free honor by selling prisoners to the night's watch + properly sharing loot and burning corpses, even with the relation hits it's possiblle to counter it by skyrocketing honor through those option alone. Otherwise, you have to grind quests for lords as often as possible. I'd also not recommend any lords that are not good-natured/upstanding due to how cumbersome it is to manage any other personalities.

In diplomacy, though, the best strategy was to have a permanent marshal by having a single Marshal personality lord so that guy would make proper campaigns while you are not "marshaling" yourself. But said single marshal lord requires constant baby-sitting and relation management, if you don't do it properly you'll lose said lord quite easily, and some fiefs along with him/her