I don't think it's a good idea to connect up in addition to the PL2303, as it will almost certainly be constantly driving the outputs.
It's probably best to look up ST's own bootloader - the impression I got was that it looks on all serial ports, so you may be able to hook up to USART2 and use that instead.
I'm not quite sure I understand what you're trying to do though - you know you can actually read/write flash directly from Espruino? http://www.espruino.com/STM32F1Flash
Espruino is a JavaScript interpreter for low-power Microcontrollers. This site is both a support community for Espruino and a place to share what you are working on.
I don't think it's a good idea to connect up in addition to the PL2303, as it will almost certainly be constantly driving the outputs.
It's probably best to look up ST's own bootloader - the impression I got was that it looks on all serial ports, so you may be able to hook up to USART2 and use that instead.
I'm not quite sure I understand what you're trying to do though - you know you can actually read/write flash directly from Espruino? http://www.espruino.com/STM32F1Flash