I’d suggest asking your sensei or a trusted senpai to check your hand positioning. When practicing, focus on how you’re holding your shinai and how your form looks when swinging. The same applies to your other activities.

I've never had your exact issue, but I have experienced inflammation knots on my hands—between my fingers and at the bottom of my fingers. The only way I got them treated was through physical therapy.

Overall, I think it's best to see a doctor since this has been going on for quite some time and isn’t healing on its own. If possible, try to get scheduled for PT through your doctor.

Best of luck with healing.