No, JB Extreme will not interferre. Start with this since you had issues with the previous Update install, download this file and extract it to your desktop and "run" the run.bat file, and install the Stock Recovery on your device. Once the Stock recovery is installed, go into your App Drawer and open OTA Rootkeeper and backup SU with the Temp-UnRoot. Then go into the Settings> About phone> System updates and download and install the Update. Let it go through should be nice and clean, after it reboots, restore Root and check my earlier comment to ensure that the System Version is 9.18.79 and you have the .15P ending new Baseband.
Will I be able to flash TWRP back on after I take the update? Also, will I need to reflash the JB extreme theme? Thanks btw