I have the 3.9fb bootloader from iliberty .... should I tick the upgrade to 4.6 bootloader option when creating custom firmware ? or should I just leave it alone.

I was on 3.9FB and I ticked the 4.6 option. Installation worked fine. It looks like I'm on 4.6FB now.

can anyone else verify this ? i want to be sure before doing something that can brick my phone.

If you're really that scared, you shouldn't use this tool anyway as it changes your bootloader.

I didn't check any of those tickboxes on the initial pwnage, and just told it to unlock the baseband.

Then when my custom firmware had finihsed flashing, I then used BootNeuter to go from 3.9FB to 4.6 original (neutered of course!) - worked perfectly

I also did 3.9FB to 4.6, no problem(s) at all.

I did 3.9 Ori to 4.6 Ori and back and it works perfectly