As promised, the detailed logs. Just for reference for others like me that are still noob about all this.
My phone spec: Xperia Z1 C6903, running 4.4.2 KitKat, on firmware 14.3.A.0.757 (no root, locked bootloader).
-Root, Backup TA, Unlock bootloader and more! The ultimate Xperia Z1 guide
-[25NOV][FLASHTOOL GUIDE] HOW TO for n00bies - G-FACE GUIDE
-[STOCK][C69XX][4.4] Update to 14.3.A.0.757 [Root & XZDR][DE-/ODEX]
-[DEVDB][TWRP][PhilZ Touch][CWM] XZDualRecovery 2.7.1XX RC
-Installed adb and USB driver (from Android SDK), Flashtool 0.9.16.0
-Phone charged to 90%+, enabled USB debugging, stay awake while charging
-Downloaded all required files (C6903_14.1.G.1.534_NUT.zip, C6903_14.3.A.0.757.flashable.zip, C6903_14.3.A.0.757_Stripped.zip, Z1-lockeddualrecovery2.7.123-BETA.installer.zip)
-Made backup for all my data including apps using Backup & Restore, saved into SD card
And here's the step-by-step of what I did:
1. Preparing 14.1.G.1.534 firmware
-copied C6903_14.1.G.1.534_NUT.zip into "C:\Flashtool\firmwares\"
-changed the extension from *.zip to *.ftf (C6903_14.1.G.1.534_NUT.zip --> C6903_14.1.G.1.534_NUT.ftf) for it to be recognized by Flashtool
-already flashed this firmware when I read eclyptos' suggestion to change the extension, so I hereby confirm that it's working!
***NOTE: Downgrading to .534 wiped out my data on internal storage (not SD card content though). Didn't know that, thought only unlocking bootloader does - good thing I've made backup of all my data beforehand.***
2. Flashing C6903_14.1.G.1.534_NUT.ftf using Flashtool
-just followed instructions on Flashtool, turned off my phone, unplugged from USB, then connected again in flashmode (using instruction in guide)
-flashing started automatically once it's connected in flashmode
-flashing done, phone turned off automatically, unplugged from USB, turned it on
-phone now on JB 4.2.2 with .543 firmware but no root access (verified with Root Checker)
3. Installing XZDualRecovery and root access
-extracted Z1-lockeddualrecovery2.7.123-BETA.installer.zip, ran install.bat, chose option 3 (installation on unrooted ROM)
-once done, phone rebooted automatically into default recovery (PhilZ Touch), chose "Reboot Now" with 2nd option to install root access (SuperSU)
-rebooted, phone now has root access (verified with Root Checker), with BusyBox v1.20.2-jb "static (2012-11-25 17:47 +0100) multi-call binary" (wasn't sure if required to have root before upgrading but tried it anyway)
4. Preparing to upgrade to 14.3.A.0.757
-copied C6903_14.3.A.0.757.flashable.zip into SD card, C6903_14.3.A.0.757_Stripped.zip into "C:\Flashtool\firmwares\"
-changed primary recovery to TWRP using NDR Utils app (pre-installed in .543), tried to reboot into recovery but reboot not working (nothing happens)
-rebooted into recovery again using adb command line ("adb reboot recovery") - Google FTW!
-rebooted into TWRP recovery
5. Flashing C6903_14.3.A.0.757.flashable.zip using TWRP
-on TWRP, chose Install, navigate and chose the file
-tried with zip file signature verification, failed
-tried again, without signature verification (MD5 check), successful
-firmware update started, took a while and done successfully!
-DID NOT REBOOT (as per instruction in guide), back to Home->Reboot->Power off, unplugged phone from USB, turned on phone
6. Flashing C6903_14.3.A.0.757_Stripped.ftf using Flashtool
-connected to USB, renamed C6903_14.3.A.0.757_Stripped.zip to C6903_14.3.A.0.757_Stripped.ftf, started Flashtool
-flashed everything in the FTF just like in step 2, phone turned off automatically once done, unplugged from USB
7. Verifying upgrade
-Phone turned on, Android is upgrading, optimized apps, etc
-Phone now back to 14.3.A.0.757 firmware but has ROOT access using SuperSU (verified with Root Checker), with bootloader still locked!
Will backup my TA partition later, but I'll just leave the bootloader locked for now. Restored my backup, checked and re-configured certain apps settings, no weird behavior so far, camera and wireless also working fine!
That's about it. Hope this log will help others to have root on their Z1 of same spec. Good luck!