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> First problem I get is that uploading the .tgz file to the new server is a real pain. SCP fails (slows down after a few seconds and then stalls completely) but FTP works at an acceptable speed.

You need to disable the "Optimize Buffer Size" feature of WinSCP which is incompatible with the upgraded SSHD included with the Gaia 3.10 OS, see here: sk163940: SCP/SFTP file transfer is very slow after upgrade of SSH

If you are saying the MD5 sum of the file didn't match after FTPing it that means you did not set binary mode for your FTP transfer and as a result of using the default ASCII mode the config file is now corrupt, which is why the import is complaining.  Fix the buffer setting in WinSCP and use that to transfer the file as it defaults to binary mode by default.  Your import should work at that point.