Well I'm happy to say things have improved tremendously!! Jaxon has more of a routine down and has been consistently going outside first thing in the morning (pees and poops). He's been hitting the paper 100% for pees when inside, and I'm started to figure out when he's 'asking' to go out. It's very subtle but I'd rather take him out more often so he gets it right.
I confined him for a couple of days last week - he really didn't like it. If I left, he'd crash his food dish so the water would spill out and the crunchies went everywhere. Now that he's back on track, I'm not confining anymore. As long as he gets it right, he gets freedom.
Hopefully another week and we'll be perfect!