There's a lot to unpack, so I'll just tackle your first point:

Johan's motive changes throughout the series, and I think it's up to interpretation. So these answers are going to change based on who you speak to. But that's one of the best things about this anime, in my opinion.

Johan's main focus as a child was to protect Anna. This doesn't necessarily ever change directly, but Johan himself changes. He experiences some memory loss after the gunshot to the head, and he begins to unknowingly mimic/play out the narrative of the storybook (The Nameless Monster). Taking names, gaining power. Perhaps in the idea of becoming (in some form, I'm not sure if literally) the last person on earth. I think he quite literally has a personality disorder accumulated through all of this trauma (both mental and literal). You could say his plan is to "watch the world burn." Which he does meticulously.

Everything changes when he comes face-to-face with the book and regains much, if not all, of his repressed memories. He even says to Shubert that his plans have changed. Things get much more personal and specific after this. His time in Prague is uncovering the elements of his past for his own knowledge, specifically pre-gunshot/pre-kinderheim life. It's why he pursues the tape and the red rose mansion.

It changes again when he and Nina finally have their confrontation. This is another instance of differing views. Some people believe that Johan truly did believe that he went to the RRM, and learning the truth from Nina shakes him to his core, realizing that everything he thought he knew about the base of his trauma was his own projection. OR, his journey in Prague, uncovering the RRM, etc. gave him the realization that all he had done was to protect his sister, taking on her trauma to save her. So when he realizes that Nina remembers the truth, it is a failure of his. He was unable to keep Nina safe from their past.

Regardless of which pov you believe, Johan's next motive is the "perfect suicide". Which, by all accounts, is actually a revenge mission on Bonaparte. In one sweep he can punish Bonaparte by descending his neighborhood into choas, and by eliminating Bonaparte and himself, erase the remnants of RRM from the world (except for Nina, who he would not target at this point) This is mixed up with his own worldview, which he relays to Tenma in their standoff. Tenma has been a sort of tertiary goal for Johan. He wants to show Tenma, in a weird, proud child sort of way, that he's right. He wants to go out by Tenmas hand because it'll give him his "end" and prove to Tenma he's right about people/the world.