Hi there
May I suggest a gate for the kitchen or an xpen instead of the crate? That is a really long time to keep a puppy in a crate.
It just takes time to get a yorkie trained. I've come to realize that. They can even regress sometimes.
I would just start from the begining. Keep access to only one room available for him. Put pads down all over where you have him. Then he has no choice but to use the pads. Then, gradually, pull pads up until you have one where you want it.
At 6 months old, he may be marking instead of peeing. Is he neutered?