Well I recently bought an Iphone for my girlfriend and our anniversary. It was already jailbreaked and unlocked so it worked with any SIM. I advised her NOT to update through iTunes but she does.

So now I'm stuck with the 3.1 firmware, with a baseband of 5.11.07 -I believe- and a 06.02 bootloader.

I know I can't downgrade the bootloader so I can jailbreak and unlock, at least for now, but I'm curious to see if it is possible to build a custom ipsw with a lower firmware version with a any of the bootloader I see around -3.9 and 4.6 I think- so when installing it via iTunes and DFU mode it can change the bootloader.

I don't even now it what I'm asking is possible and if it is, if it will change the bootloader.

Any answer will be appreciated.

What you are suggesting will either plain fail or permanently brick your phone. The two baseband bootloader versions you mentioned are for 2G iPhones and are not compatible with 3G iPhones. If you don't have 5.08 baseband bootloader then you have no way to downgrade the baseband.

You are out of options right now. It will be a long wait until an unlock for 5.11.07 is available - if ever -