Yeah just remove upload_tool = .. and it will default back to flashing via UART. You need to put back one of the interfaces in UART mode so that the PC sees a COM adapter, connect the wires for UART RX,TX, IO0 and EN as seen in https://github.com/espressif/esp-iot-solution/blob/master/documents/evaluation_boards/ESP-Prog_guide_en.md?utm_source=platformio&utm_medium=docs and it should flash it.