Hi Shulong
Yes, the USB and FFS are not included into MQX 4.2 clone wizard for K64.
MQX project cloning is just pasting and copying some files. you can do it manually. (only copy usb and ffs , and others you can do it with MQX clone wizard) Please read the following document,the attached document guide you how to do it step by step.
Re: Custom BSP for MK20DN512
Regarding the USB stack, I think USB_V2 is better, it is a new design, and has less issues.
Regards
Daniel