There's been ~160 chapters, perhaps 7 Major Milestones, and the SRD
suggests having a Significant Milestone "when in doubt, at the end of every two or three sessions" (which I'm going to arbitrarily translate into every 5 chapters and see how that looks). So, 80 skill points and 7 points of Refresh/new Stunts (two updates a week for near two years is a lot of chronicle!).
One of the less obvious rules is that there's a skill cap (defaults to +4, though given ninja are absolutely superhuman it's most likely pushed to +5 or even +6) that you can only raise at Major Milestones, so that suggests Hazou can't have any skills above +11/+12/+13 (depending on starting cap). This may be slightly awkward in a game that assumes characters won't generally go past +8; we'll see how much it matters. Finally, given the sheer number of points (and level of specialization the characters should be able to pull off), the skill column won't be able to hold up forever - I'm going to be kinda arbitrary about it here, 'cause I haven't settled on any ideas I particularly like as to how to systematically move past it.
High Concept: Idealistic Ninja of the Leaf (Still dedicated to his high ideas, but with a new home and allies)
Trouble: Social Outsider (Much of Leaf may now see him positively, but he's still an outsider, and still socially awkward at times)
Aspects: Relentless Optimizer (as above), Team Uplift! (fairly self-explanatory), Hold the Line (as above).
Stunts: Ninja (as above), Iron Nerve (as above; 2 pts), Roki (as above), Sealmaster (exact mechanics TBD, but "able to research and create seals" should cover it for now)
(possibly more Stunts, but pretty much everything else he has or does is jutsu, which are their own thing; maybe some kind of upgrade/sequel to Sealmaster? He's got more than enough Refresh to buy a couple)
Refresh: 9
+8 (Legendary):
+7 (Epic):
+6 (Fantastic): Melee
+5 (Superb): Athletics, Deceit
+4 (Great): Chakra Control, Chakra Lore, Alertness
+3 (Good): Chakra Capacity, Infiltration, Physique
+2 (Fair): Provoke, Empathy, Rapport, Willpower
+1 (Average): Survival, Investigation, Medicine, Ranged, Crafts
So, that's 30 points spent (which is, on the outside, about 90 sessions of tabletop game worth), and that seems to be as far as the column takes us (without adding filler +1s that Hazou really hasn't bothered with, like Administration, and there aren't many of even those left to pick from). The funny part is, glancing between this and Hazou's character sheet, I think it looks pretty accurate. He's terrifying in melee, tricky as hell, solid at using his jutsu, and vaguely socially competent when not lying.
I'm honestly not sure how to handle the remaining 50 skill points - maybe allow you to buy a skill above where it should be in the pyramid for extra points? Maybe add a mechanic where skill points are involved in buying jutsu, or make jutsu-specific skills? The answer, I believe, has to flow from what you want a top-level character to look like - figure that out, then figure out what sort of rules would incentivize (or at least support) building them (sadly, no ideas here as of yet in that direction).
Some of these issues are because this is translating from a system where individual jutsu cost xp to one that doesn't (which I do think fits the fiction better - higher-ranked jutsu specialists are portrayed as having a fair variety, but even with secondary-jutsu-of-that-element discounts it seems odd they'd have more than a couple, especially for elements like Fire where canon mostly boils down to a bunch of different ways to shoot fire out of your mouth). Some is just the fact that MfD is a game that's been running for a long time, with frequent updates, in a setting with a high power ceiling, and "start running into power ceiling issues after 90+ sessions of game" is hardly unusual. I've certainly had D&D games hit level 20 (the usual cap) in much less than that (seriously, that's almost two years of weekly sessions worth by itself, which is pretty long for a tabletop chronicle).