I see this forum is not super populated. I will look into your phones requirements, but, I pretty sure if you just want to flash/install an update to your custom ROM all you have to do is get into your custom recovery and wipe the cache partition and the Dalvik cache (usually found in the advanced section of the custom recovery. Then go to "install zip from sd card" select "select zip from sd card". Scroll to where the Update to you custom ROM is and select it. After the install go back to the custom recovery's main menu and select "reboot system now". It will take anywhere from 5-10 min on the first boot up into the new ROM.

Note: Make sure you use a file manager to browse where the ROM is downloaded to before you go into your recovery. I usually take it out of the folder and just move it to somewhere near the bottom of the list of folders. In the recovery when you are selecting the ROM in the sd card, you can scroll up to get to the bottom quicker as it's a looping scroll.

EDIT: If you want to flash a factory upgrade to the original firmware it will revert your phone back to an unrooted state, and root will be almost impossible(not totally, just almost).