Thanks.
Just try using Case 1. I didn't take out the USB boot. Instead I
1. mount the synoboot2 to a tmp directory
2. copy the zImage, rd.gz, extra.lzma to synoboot2
3. umount the synoboot2
3. login to the DSM, click DSM update to DSM 6.2.2-24922
4. It will restart twice
5. All ok except the esataportcfg/internalportcfg/usbportcfg in synoinfo.cfg need to modify back to N54L setting. (I use both disk5 & disk6 as esata so I set
esataportcfg="0x30"
usbportcfg="0x1fc0"
internalportcfg="0xf"
then reboot one more time my disk6 come back as esata disk