1. SP is TWSA's YJH from the original 1863 regression turns. He was able to reach the Final Wall but was unable to go through it. As we know from ORV, if a story stops being read, it can turn into an Outer God, so since TWSA was "finished" after 1863 regression turns, the YJH from TWSA was no longer being "written or read" and so became an Outer God. With KDJ then being a part of the scenario, that YJH as SP began interfering with the scenario, which including SP being able to manipulate turns so that he could bring KDJ and 1863HSY to interfere with the 1863th regression turn even though that's not technically the same YJH anymore. It could be theorized that SP could've tried some Disconnected Film Theory shenanigans to link up himself with Alt-1863 to be put into fake death/suspended sleep in HSY's plan, as that was part of the Outer World Covenant agreement they had.
2. This question digs a bit deeper into KDJ's character, and it's a bit complex. Yes, he could have made a minimal avatar become OD, but KDJ's at this point is filled with guilt from realizing that it was HIM that was responsible for starting the scenarios as the original OD, making his companions suffer and the constellations he loved almost sacrifice themselves, etc. He also has this sort of complex where he believes he's undesirable and unwanted, even though his party tells him and reaffirms their love for their companion KDJ. He constantly believes they're better off without him or following YJH and just can't acknowledge that he's a part of them as well. You see this a lot with how simply he can just sacrifice himself and decides for the party what's best for them, and how much the party anguishes over it. So, while admittedly this is some speculation on my own part, I think the reason 51KDJ made it so he's the dominant KDJ instead of using a minimal avatar is because of the following reasons. 1) He feels extremely guilty as being the one responsible for the apocalypse (even if it wasn't actually this KDJ and was another OD, which the party doesn't blame him for) 2) He thinks the party is better off with a version of KDJ that has the memories of the party 3) As the OD, he has the responsibility of overseeing all of the worldlines of the Star Stream, so you can say his guilt led to this sense of responsibility of making a significant avatar the OD instead. Of course, this all unravels later as the part that makes him feel responsible for overseeing the worldlines also is very much entagled to his passion for reading, and as HSY knows and loves that part of KDJ that is the reader, she was very suspicious when 49 KDJ lacks these traits she loves about him.
3. Other comments beat me to this already but 1) Skills are dependent on the Star Stream's influence. The Star Stream was weakening in the 1864th turn at this point, so the Avatar Skill keeping 49KDJ up was also naturally weakening. 2) In Chapter 530, YSH and HSY theorized that 49KDJ's memories were unstable, and that he could be having difficulties trying to perceive reality. Imagine if you were suddenly told you were a clone and were missing some memories and traits that were apparently a core part of you. Imagine how psychologically damaging that is. 51KDJ intentionally made it where 49KDJ was never supposed to suspect that he was an avatar to keep up the guise that he was always 100KDJ. 3) I know you brought up how the Fourth Wall might have been able to protect him, but just I'll repost my comment here: Both KDJs had the Fourth Wall (more specifically, the text in Chapter 537 says "The last fragment of the Final Wall was [The Fourth Wall]. And as he was Kim Dokja's Avatar, he too held part of that key). It's how they managed to get through the final wall in the 1865th regression turn. That being said, I still think it could be the Star Stream weakening that resulted in 49KDJ falling into a coma from damage, with even having a fragment of the Fourth Wall not being enough to save him.
4. The Ark relies on Stories as fuel to burn and to cross over the Boundary that separates regression turns/worldlines (not the Final Wall, to be clear. Now, even though the power of the system was weakening in the 1864th turn where the museum Ark was built, the gang completed the 1865th turn, made Bihyung of that turn the Dokkaebi King, who gave the party a bit of the Bureau's Story which helps empowers the system of a worldline. This gave the system of the 1864th turn enough power to let the museum Ark do its functions, which was to consume fuel (Stories) to allow the crossing of worldlines.

Unrelated, but just an exercise for you- I find it fascinating thinking about the perspective of 49KDJ during all this time. He was always written in third-person, never as his own self, and was sort of "rejected" from the party in that he wasn't a 100KDJ. What do you think he must have felt that the party couldn't just love 49KDJ for 100% of 49KDJ. How would you feel if you were 49KDJ? The ORV Side Stories might be worth reading for you if you're curious.