I am not sure why the motor is still jittery after swapping the middle two wires, unless you still have the first swap of wires 3 and 4 in place. It may be best to test with the current adjust potentiometer set near the center of the range. It can be reduced to a lower setting after you get it working. The clock needs very little current and there is no need to overheat the motor or stepper driver with extra power.
The jumper positions are documented in the sketch and should also show up in the serial debug monitor.
Here is the code. The 4x2 header block defines the modes. Your photo shows 1110 which is a debug mode to rotate the motor, but not at the proper speed for SP6, which should use 0110.
Jumpers in the 8 pin header set speed or set up debug modes
CoolEN selects debug mode if inserted
Resume, Hold, and Abort set speed to one of 8 speeds
Parameters calculated any time jumpers are changed
Motor speed settings (subject to change)
0: 0000 1.000 RPM reserved
1: 0001 4.630 RPM SP10 with 200 step motors
2: 0010 4.630 RPM SP10 with 400 step motors
3: 0011 3.600 RPM SP6 with 200 step motors
4: 0100 4.667 RPM SP9 with 200 step motors
5: 0101 6.944 RPM SP11 with 200 step motors
6: 0110 6.944 RPM SP11 with 400 step motors
7: 0111 20.00 RPM fast debug mode
Debug routines
8: 1000 LED off no test running
9: 1001 LED on simple hardware test
10: 1010 LED on simple hardware test
11: 1011 Delay test LED will blink at 1Hz (0.5s on, 0.5s off)
12: 1100 LED on simple hardware test
13: 1101 RTC test LED should blink at 0.5Hz if RTC is working
14: 1110 Rotate CW Rotate motor one direction at medium speed
15: 1111 Rotate CCW Rotate motor in opposite direction at high speed