Hi, I am experimenting with a Black Pill (STM32F401CE) and I got it to work (using USART_2).
Like you, I modified optenusart2.yml / optenusart3.yml (disabled USART_3 by changing to False, enabled USART_2 by changing it to true). Additionally, I changed the file optoschse.yml as my Black Pill has 25 MHz clock. Lastly, I changed the linker settings (in bsps/arm/stm32f4/start/linkcmds.stm32f4) to reflect the smaller RAM (96KB) and Flash (384KB).
I built the BSP manually then with ./waf configure --prefix=<RTEMS compiler path>, ./waf and ./waf install. To make sure the configurations are right, I checked the file 6/arm-rtems6/stm32f4/lib/include/bspopts.h to see if HSE and the USART was correct.
To run the application, I needed to apply a trick still, that I got from another post here in the forum. For the application to run with the debugger, first a .bin needs to be generated from the .exe (as mentioned in the post linked), then loaded with your tool of choice into the Blackpill, and only then the debugger can be run.
So comes the question, have you changed the HSE Clock as well? Normally the Black Pills have 25 MHz clock, safe some rare F411 with 8MHz. Those latter do not need modifications in the BSP with respect to clock, but the former for sure do.
All the best!