I didn't fully understand why you lost SSH access to your instance, what were the steps that you performed before losing access? If you have the key and you didn't do something strange in the instance, you should continue having access to it.
In case you don't have SSH access to your old instance, you can try the migration process without copying the configuration files, please note that you'd need this step in case you didn't modify them in the old instance. Once you copied the backup that the Akeeba plugin creates, you can import that file in the new instance and skip the steps that copy the .conf files from the old instance.
Let us know if you have any questions.