Is there a spare pin there that you could set up as LED1 in the board python file?
When starting Espruino should flash LED1 once during the init process. Usually Espruino disables JTAG/SWD on those pins so they're available for other stuff (https://github.com/espruino/Espruino/blob/master/targets/stm32/jshardware.c#L1228) so the fact that is happening is actually good news - it's running at least some code.
What could be happening is that the oscillator is set up wrong and the CPU is actually running at the wrong frequency. Do you have an oscilloscope or something you can put on the TX pin? Espruino should transmit some text at boot and by looking at it you could see if the bit rate is actually 9600 or if it's something else.
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