Agree about the call at 2nd. It was a close play and he may have been safe but as an ump you've got to make the call immediately and stick to your guns like you're 100% sure it was the right call...
The knee thing was a two part issue for me... First, he intentionally tried to get hit, which is ******, but as you said, from his view point the ump may not have seen it. The part that got me was that the pitch looked like a strike. In fact, I originally thought he called the guy out on strikes. If it's that close to a strike, there's no way his body wasn't in the strike zone.
But the balk was ridiculous... the guy kicked his leg forward then threw over to first... Balk, for me at least, are normally hard to spot in real time. That was one of the most obvious balks I've ever seen.