Hey there Isaac! What kind of neck do you play on? I once played on a friend’s guitar (who she had developed a repetitive stress injury from playing) and I couldn’t even play on it for 10 minutes without my thumb hurting. Her neck was super thin. Way thinner than what I was use to. But for her, it felt like nothing until three or five years after playing. Is there anyway you could get your hands on another guitar to see if it hurts as bad? Keep in mind, it will STILL hurt to some degree if some stress damage has been done.
Also, there’s a student on here who made a GREAT video about the “Most Pressure Needed”. After watching his lesson, I realized I was gripping the fuck and squeezing the hell out of my neck when I didn’t need to. Perhaps you could evaluate your pressure?
Lastly, be sure there is no weakness in the finger muscles, hand muscles or arm muscles that would encourage your thumb muscle and joints to make up for it. I hope this helps. Music is my life too, and I hope we can catch whatever this is early!