From your error message, I think the default set of key objects that comes in any SW are also deleted. So the key/cert folder is completely messed. As you could see when you try to load the default config, it tries to restore the default set of objects and any referrenced object missing will cause the load to fail.
Luckily, this load actually looks for referrenced object alone, so you can simply touch the files to be created and hope for the config to be reloaded properly. Just make sure those dummy referenced configs are not used anywhere when you go live. Else you have to install in new volume & move forward. So when you boot into that, select no forward configuration in GUI. So it will be a clean slate.