Thanks for the reply luacs. It appears to accept commands when the server is actually up and ready for players, but I don't make it that far. I've tried to get into McMyAdmin as soon as it starts and enter the command but it doesn't appear to do anything.
I just wiped Millenaire out and restarted a world. I got tired of Version/Error/BackupCraft.
I've read MY log and I still can't figure out how to issue "/fml confirm" to Forge. I've tried doing it through McMyAdmin (it's hosted), through an RCON session and through the server config file. I'm not sure what needs to be edited to get the server to start. Basically I removed Millenaire and it has a bunch of blocks missing. I don't care if they are turned into air. Is there a better way to do this?