MC doesnt matter in the 3GS sense, only important for ipod touches, anyways how did you originally jailbreak? if you used pwnagetool or redsnow then you can use pwanagtool 4.01 to create a ipsw and then simply restore to it in itunes (better to put your phone in recovery mode). also you have to check your bootrom (tethered jailbreak?, new bootrom, where you had to connect your phone if the battery died, restart, etc.)
helpful info from dev team:
iPhone 3GS
Summary: Currently, PwnageTool only works on previously jailbroken 3GS devices with the old bootrom.
If you have a Jailbroken iPhone 3GS with the OLD BOOTROM and you DID NOT use Spirit to jailbreak then you can create the ipsw with PwnageTool 4.0 and restore with your jailbroken recovery mode.
If you have an iPhone 3GS with the NEW BOOTROM this is NOT supported by PwnageTool 4.0 PwnageTool 4.01