Don't worry in the slightest about Raiga. As I stated above, this character is not the same Raiga from the Anime. The picture of the manga 'Raiga' was of a 2 generation old swordsman. This means he predated the last wielder of the lightning blades.... who obviously died before the series began. This means the manga 'Raiga' died even before that, proving his filler arc is just that; filler. We can't even confirm his name is Raiga as Kishi never gave it.
Keep in mind, old databook information is not necessarily canon as it was created so long ago that its wording should not be taken as literal. Obviously things like the description of Itachi's Susanoo shouldn't be taken literally because his defense isn't truly impenetrable. Things like academy graduation ages were used for a sole purpose, to prove strength.
Before Kishi could describe the skill level of a Shinobi, he used graduation ages to explain it. This was obviously a dated and imperfect concept for obvious reasons. He told us Kakashi graduated younger than Obito in order to show us he was stronger than Obito. Later on, he adopted the 3 person team ideal and changed this fact to better match his story. In short, there is no discrepancy in academy ages and graduation, its a very straightforward concept that they were all the same age and graduated at the same time and hence how they ended up on the same team. It was made more clear once Kishi's ideas were better developed, which indeed involved editor influence.
Yagura was never confirmed to be on good terms with the Sanbi and Madara was the original manipulator of him, so its not impossible to see this as fitting into the story. I'd argue that Minato's face on the monument in the wrong era was a part of a greater attempt at deception by Kishi, but most likely it was just a significant mistake on Kishi's part. That is not a plothole, just a blunder.
