if can switch on then you should not worry. yup flash tru flashtool very risky. my phone almost bricked once.
i believed you have unlock your bootloader before right? sorry i lazy to go back to previous page to read your previous post 

root will be lost once you flash with official ROM, both GB and ICS, but once your bootloader is unlocked, flash with flashtool wont lock your bootloader back.

do you still want to update through flashtool? if not, ignore this post.

to avoid flashing rom using flashtool goes wrong, these are things that you have to make sure. (double check, or even triple check).

1. have you install necessary drivers? just reinstall just to make sure. go to flashtool folder where you install the flashtool, open drivers folder and install "flashtool-drivers"
2. does you have correct file? doublecheck with md5 checksum for error. redownload if the file is corrupted.

i know you have try this step, but please double check the step.

1. switch on your phone, make sure USB debugging is on. make sure also your connectivity setting set on MSC, not MTP
2. try connect your phone with usb. the phone should detect USB debugging mode. the computer will detect the phone "ADB mode"
3. now remove the phone, switch the phone off.
4. hold back button, and connect your phone tru USB. green LED should be on right now. now it is in flash mode.
5. your computer should detect your phone.
3. if no ADB driver, that mean you haven't install the necessary driver yet. please refer up to install the driver.
4. if everything ok, pull your phone from the phone. switch on the phone.
5. open flashtool using admin (make sure you use correct 32bit or 64bit version)
6. connect your phone
7. flashtool should detect your phone. (they will tell you the MSC setting, USB debugging mode etc)
8. click on thunder icon
9. select flash mode
10. select your ftf file. (note that default folder is at X:\Flashtool\firmwares, change your source folder accordingly)
11. and they will ask you to remove your phone, switch off the phone
12. remove battery and put back battery
13. press back button, and reconnect back your phone tru USB (don't switch your phone) green LED light should on now.
14. the flashtool will detect your phone
15. wait till it flash your phone.
16. after it finish flashing your phone, remove cable, and switch on your phone. PLEASE WAIT PATIENTLY. it usually take up to 30min for first time boot. you may charge your phone but IMHO please dont connect to PC.
17. viola.

usually
if can't detect your phone - driver problem. (reinstall driver, download new driver)
if brick/bootloop/blank screem - file problem (redownload necessary file should correct this)