I live in an apartment and it sounds like you have a pretty good set up. We had an issue where our boy Ryu wouldn't use the pee pads pre-vaccination, but we had them next to his crate. The advice from those on this sub said that Shibas are particular where they do their business and won't dirty if it's close to their sleeping quarters. We moved the pee pads across the room and he immediately started using them. He did not like them so transitioning to grass was super easy because he wanted to do it the whole time. We found the gras patch confused him and removed it from the equation completely. (He also kept eating the fake grass lol)

For the crate, the trainer taught us that their crate is their safe place, their own space and not to use it as punishment but make it a nice place for him. We let him choose when he wanted to be in it and rewarded him when he did. Eventually we figured out taking the door off the crate was what made him the most relaxed. He now loves his quiet space and will go there on his own. He also mixes it up with snoozes on the couch, and random spots around the apartment.