That first loop was certainly completed, and while the second is debatable, he does another clean loop in the opposing direction of the first one, later in the sequence. There's no rule against going up towards the toepick for choreographic effect during a loop; he does a full turn on one foot without switching edge, the entry and exit are there. Loop turns are often boring and kill the cadence of footwork; being able to do them in a quick interwoven motion shouldn't be shunned. That counter turn you brought up was fine too; starting on a deep edge, not swapping over before the transfer, and exiting on the correct edge on one foot. Should be watching a better quality video, btw! I also never brought up the Level 2 call on Takahashi's last spin, it's very sketchy they didn't credit his pike sit position. He was in a good enough position for 2 rotations, particularly considering the pike positions from many other competitors (especially Plusenko) that got credit.
I was hoping for more discussion from people about the specifics of the programs that caused them to grade the PCS as they did, or individual elements. I could have been a bit more generous for Kozuka's PCS in the LP, his demure qualities sometimes make his actual skating seem less difficult than it is, and the drive and deep flowing edges and emotional authenticity in that performance impress me every time. He was also the only guy in the competition to land each type of different jump (considering "Quad" as a jump type). One example of an annoying CoP feature, though, is the edge change he had to do in that last spin to get a level 4; it makes the last part of the spin and final pose fall just a little out of step with the music. A good scratch spin like the one he did should count for level credit, bah.