Hey thanks Erich for your fast reply as well as yours wonderful and details blogs.
Honestly I buy this board by referring your blog only, they really helpful for newbie like me.
now what you have suggested to update firmware/bootloader was already successfully completed. please refer following image of SDA_INFO.html

I started with teensy3.1 which has MCU(Mk20DX256VLH7) of same series, I develop very stable firmware by teensyduino (Arduino Add on) which also giving accurate results for my project. Now I have to integrate all pcbs including teensy. when I build my code, teensyduino generate .elf file for particular code, and by referring your document and search I came to know that I can flash my code to my custom board with openSDA of FRDMK20D50M and USBDM.
Yesterday I developed Blink.cpp.elf file for simple blink LED code from teensyduino IDE and Flash that file in Target on-board MCU with help of USBDM and its working perfectly. I have not tried on my custom board yet, but I guess It also work by doing some hardware changes on board (cutting J11 i.e. Swd_clk).
my end application firmware will only includes SPI and UART over USB-CDC. Hence I also tried by flashing .elf of Uart code in same way as above but its showing like usb device descriptor request failed when I connect to USB-CDC mini usb as shown in fig.

Also when I simply tried with blink LED. elf at that time it does not show any hardware changes in device manager.
So in summery my open SDA USB virtual com port is enumerate successfully but it fails with USB-CDC.
Thank you
HD