Part Number: PINMUXTOOL
The online pinmux tool likes to walk all over JTAG. It seems to want to do it by default on the devices I have used so far. Is it possible that in a soon-to-come iteration of the PINMUX tool that you could allow users to reserve JTAG pins for JTAG? What I've had to do was assign JTAG pins to GPIOs, then carefully cut them out of the resulting pinmux.c file that's created by the tool. I really shouldn't have to.
This all just goes to show that "TI doesn't do software" ... which is exactly what I heard pretty much for my duration of employment in TI, as a software guy.
Please fix your tool, it's painful to use.