It could be a software issue. You could try updating or just restoring the phone all together. If that doesn’t do anything I would replace the charging port and headphone jack ribbon cable. Here is a link: iPhone 6s Lightning Connector and Headphone Jack
Sounds like it could be a logic board issue. I would also check to make sure all the of screen connectors are properly inserted first. If they are fine and you have swapped the battery and it is still experiencing the same issues either the logic board could have a defect or the pads where the battery contacts the board isn’t getting a solid connection. If you have a spare board lying around it wouldn’t hurt to swap it. Issues like these are hard to diagnose because if you are like me you don’t want to blow $100+ on a part that might or might not fix the issue.
Make sure you got a good contact with the heat pipes after you reapplied the thermal paste. If that is not the issue than, the only other thing i can think of is the cpu fan isn’t working properly or it is a software issue. I don’t have a whole lot of experience with Manjaro so I wouldn’t be able to help you there.
It is probably the earpiece speaker that is going bad. Make sure the front facing camera and the proximity sensor are working. If they are both in working condition, I would replace the earpiece speaker first. If the camera or proximity sensor is not working, it is most likely the cable that contacts the earpiece speaker. Both of these parts are inexpensive and the repair is pretty straight forward. This is the link for the ifixit tear down of it, Remplazo de Auricular de Pantalla de iPhone 6s