I cannot cover any of the calculation sections as I didn't do this calcs and they aren't my expertise, so I'll just cover the abilities for staff.
1. Limited Durability Negation has already been covered extensively throughout the thread, but I'll provide
the scans for it. The first instance is a bit weak, with the punches being described as "piercing," but then it's corroborated with an explicit visual showing of the force of Yu's blows travelling through his opponent, both in the instance of John Taker and with Yuto Takeda, we can see the shockwaves literally blowing through their body in a way that wouldn't happen with typical blows. Normally Yu's blows make a person's head blow up so we know this isn't just an action of raw strength at work. And we also know that these shockwaves are real shockwaves (for obvious reasons that are obvious). It's not actual dura neg, of course, it's limited in that it can only partially bypass things like guards or defense to make attacks hit with more force, but that should still qualify. Yu also gains the ability to actually internally damage his opponent's organs, even against characters he can't even budget with normal punches, by training this piercing power.
2. Analytical prediction. I'll just provide
the scan for it here, but it's also on Yu's profile. This is very obviously analytical prediction. I don't think I need to explain why. As for the resistance to it, I can't get the scan right now, but long story short, all "Genius" Boxers in the series have a concept called "freedom" or "flow" that is unique to them and allows them to create their own style of optimized movements. A genius boxer, Siha Lee, is unable to predict another genius' movements due to his level of "freedom" being superior to Siha's. That's why the resistance is universal to characters who possess this freedom. The thread which implemented it is really old with blurry scans but the arguments remain generally the same.