Hi Daniel,
That is not the right path to your .TCL file, at least that is not where MQX usually has those files. The default location is \Freescale_MQX_4_0_1\lib\twrk60f120m.cw10\dbg. And after fixing your initialization file location, you will probably need to fix the memory file and path for the .MEM file as well.
It appears your Debug Configuration was altered, which has caused all these issues. I just tested the gpio_twrk60f120m using MQX v4.0.1 and CW v10.4, and it has no issues downloading and running on the TWR-K60F120M board. If you continue to have these issues, I suggest you start with a clean project, maybe reinstall MQX if needed, so the Debug Configuration will have the default settings, and you won't need to clean it up.