OpenOCD is a massive godsend for any kind of board bringup/embedded development. While I can't speak for your board specifically, if the pin assignment is soft

OpenOCD is a massive godsend for any kind of board bringup/embedded development. While I can't speak for your board specifically, if the pin assignment is software reconfigurable (and is reset to sd-card access on reboot!) and you're not using the SD card once your program is running, you could reconfigure the pins in software and then wait for a JTAG debugger to attach (by having an infinite loop you use openOCD to continue past). Of course if you can debug your issue using QEMU that's indeed much easier, thanks Fabrice!