I'd take a break (a few days should suffice completely in your case). I had a similar 'condition' and had to completely stop playing with my index finger for a month now, due to an issue with my tendon. From what I read it takes up to 3month (possibly longer) for it to recover. (While I can move my finger without any trouble, it felt very weak when I played and it seemed as though I could feel my tendon being pulled everytime I pressed a button/pulled the finger up)
If this only happens when singletapping and you got a mech kb, consider getting O-Rings. They helped me reduce the stress a lot. Alas, I got them too late and didn't take breaks either, so I ended up "wasting" months during which I could have been playing properly (currently switching between mouse only and playing with middle+ring finger, I can't tell which playstyle feels more awkward, but both have some huge disadvantages for me).
As far as I can tell, hand positioning shouldn't matter. If you don't want to spend money on O-Rings, try singletapping with less force. Even if you can't play very fast songs that way, you will adapt to it eventually and be able to do so.
(I'm assuming that you play with KB+Mouse/Tablet and that you are singletapping with your middle finger, else whatever your problem is, it is most likely unrelated to mine)
Also pain is not a sign of improvement. What the hell. Pain is your body telling you that something is wrong and you should stop whatever is causing the pain.