The third hokage and Danzo should be crucified on the pillar of shame in each and every fanfic, the fact that this MC is so chill about their deeds and even restrains his subordinates from going to give them the lesson they deserve is mind blowing and utterly wrong on all levels.
Couldn't he just synthesize the chakra fruit by getting some chakra samples (hair or flesh could be a substitute] from the 9 biju or their carriers, not it's full power or charge but pretty much give himself chakra veins or their producing equivalent