Update heavly customized but stock rom Nexus 5 keeping data?
You don't need to disable anything :-)

Step-by-step guide:


Update your recovery to the latest version
Download this 4.4.3 update and SuperSu
Place these files in sdcard
Boot in recovery
Wipe Cache and Dalvik Cache
Flash 4.4.3 update and SuperSu (~15/25 mins)
Reboot
Re-install X-posed framework from its installer
Re-install custom kernel


Now you have 4.4.3 and all of your customization without losing data ;-)