Hi Sri-
You should start with DDR_Stress_Test -- this will already validate your Power circuit, iMX6, DDR and USB-OTG.
After that, you should port UBOOT. That will already let you test eMMC/SD, Network, USB.
If you port Linux, you can test most of your board with the unit-tests Freescale provides.
JTAG you should test by connecting with a JTAG debugger.
Full testing requires testing a large sample of boards for a prolonged period at different temperatures, vibration, etc.
Good luck.
Erez