Default [Q]SDCard is missing after flash Kernel

I am using a HTC One X+ with AT&T. I have been running on ELEGANCIA™ 3.1 since I got the phone. Everything was fine expect the WIFI/Mobile Data Connection. The symptoms are:
1. Sometimes WIFI turned itself on automatically even I manually turned it off.
2. I usually use WIFI at home. Most of time when I left home for work, the phone won't automatically internet connection even the phone showed the the Mobile Data was connected. Turn the mobile data on and off won't fix it. I have to reboot my phone to connect to internet.
3. When I returned home, sometime the WIFI won't automatically get connected. I have to manually turn it on.

Since I have some many issues with the WIFI, I decided to flash the newer ELEGANCIA™ 6.3 to see whether I can fix the problem. That's when the trouble started.

I used the flash kernel feature in WinDroid Universal HTC Toolkit v1.1 to flash the boot.img extracted from the ELEGANCIA™ 6.3 package. After flashing it has no access to sdcard anymore. ES file explore shows no SDcard folder. In addtion, the WIIF can't be turned on. It shows turning on then error out.

I have very limited knowledge about Android system. I don't know what I can do to fix my issue. Any help will be greatly appreciated. Thank you.