Did you answer incorrectly in redsn0w regarding "late model device?" question? You should have answered yes. If you answered incorrectly to that, it is likely you can't use pwnagetool/custom ipsw to solve your problem.
You have a fundamental misunderstanding regarding the right terms. A quick lesson.
Baseband: the OS for the radio part of your phone (making calls, SMS, wifi etc) this is often updated with new iPhone OS releases. iPhone OS 3.1.2 came with baseband 05.11.07 and iPhone OS 3.1.3 comes with 05.12.01
Baseband cannot be downgraded on the 3GS, only upgraded.
Baseband Bootloader: the bootstrap for the baseband OS, it checks that the baseband is valid and then loads it, passing control over to the baseband OS once it is loaded. It is possible for this to be updated in a new iPhone release but it has not happened since the OS 1.0.x days. So nothing to worry about here.
Baseband Bootloader cannot be downgraded on the 3GS, only upgraded
Some reading:
http://www.hackint0sh.org/f203/109567.htm
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