On the knee strike there's not going to be a perfect answer. Examples Switch it to a knee on the canvas over hand and they will drop a knee to protect themselves. Have a ref calling a up or downed opponet leaves room for error too / fighters understanding/ hearing/ and ref missing it. Biggest thing is if it's a rule inforce it or get ride of it, as it's not fare for a fighter to follow rules and his opponet not to.
Kick to the nuts fine with once give time to recoup as a fighter has the choice not to continue. Knee to the head is more controled unless a fighter moves his head into the strike, but thats not likely.
Either way call it the same all the time will help