How to remove Cyanogenmod from Sony Xperia Z?
There's no such thing as "CM bootloader" - a CM installation only writes a new /boot (kernel) and /system.

Since you are explicitly looking to return to stock, FlashTool is still your best bet. Find the latest stock ROM for your variant and region using XperiFirm, generate a .ftf format file with what you downloaded using Flashtool with the guide here, then flash away.