Hi, Sutter,
If you have configured the JTAG port signals to general GPIO pins, it is difficult to reconfigure them as JTAG pins.
Generally, after Reset, the JTAG pins from GPIOD0 to GPIOD4 function as JTAG function for MC56F84xxx, after the DSC runs to the application code which reconfigure JTAG pin to GPIO pins, the JTAG pin function are changed.
Do you have reconfigured the Reset pin as GPIO pin? if it is the case, it is a bit difficult. You have to adjust power on procedure and CW downloading procedure so that CW can reset the chip before DSC run to the reconfiguring code.
Hope it can help you
BR
Xiangjun Rong