Sorry just saw thread feel free to e-mail me you will get faster responce as i am not on here as much lately.
Sounds like the PCV + AT are working fine,the O2 bypass plug needs to be pluged into the bikes O2 harness and never turnon ignition while you have any electrical things not contected which is probably the cause for your error code, try disconnecting the battery for about half an hour then reconnecting this will usually clear errors if you don't have TuneECU if you do then use it to clear them. Let's us know how you go.
And in answer to first question yes you are safe to ride regardless of what or when you change any thing exhaust or inlet as the AT will adjust accordingly