ok, so as a Kinetis 100 MHz MCU, the baseline BSP to clone from initially would be twrk40d100m.
This BSP has usb stack support - I mean native MQX USB Device stack. Then you just need to disable features that your K20 100 MHz doesn't have.
Check this document, it may help to create your custom BSP:
https://community.freescale.com/docs/DOC-94248
and check also the init_bsp.c (_bsp_enable_card()) function, which is the basic function to initialize hardware for a board.
Then, once you can boot an MQX system and usb device example applications with your custom BSP, as there is no CCID device class support, you will need to create your custom device class driver. How to do this is desribed in MQX USB Device User's Guide, Chapter 4 Developing new Class Drivers.
You can also follow source codes in one of the existing class drivers, like for example follow CDC device for bulk endpoints and HID device for control and interrupt endpoints.