The MCU board now lets the printer pull in the carrier until the new
paper in sensor is triggered for the first time and then starts the
print like before. The new "initial feed" provides an alignment of the
carrier which is exactly the same every time. Of course, the carrier now
needs two markings.
At first I was using the 2400dpi mode of the printer. I now switched to
the native resolution of 1200dpi because the results are way better. The
2400dpi mode can still be used if a #define in config.h is changed.