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@JeonLab
Well, I disconnected the battery and reconnected, but it didn't solve the issue with the accelerometer. I think I have done all I could try. I don't want to damage other parts, so I will stop trying to figure it out. Although I'm going to miss the pedometer, but that's not a big deal.
My main reason to design the new case and adding so many (most people won't need it) buttons and buzzer and bigger battery was for my golfing (https://banglejs.com/apps/?id=golf-gps ). Currently it uses swipes for moving the holes and adding/subtracting scores while I'm playing, but if I touch (and slide) accidentally, the score or the hole changes unintentionally. That's why I wanted to have physical buttons (left/right and up/down) and bigger battery for continuous use of GPS. The buzzer is my preference over the vibration motor.
Although I lost the pedometer, I'm happy with the other modification. I have attached some pictures to show the internal arrangement of components in case someone's interested.
The motor is moved to the right side wall in a tightly fit hole. This motor vibrates radially, not axially, so it feels much stronger than original configuration (taped on the battery). The buzzer sounds loud enough. I have tested with a MOSFET and direct drive from the pin D43, but didn't see any difference, so just connected directly to the pin D43 for simplicity. As for the battery life, I tested yesterday with continuous GPS running after full charge and it lasted over 9 hours.
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