Don't bot on an account that your'e not willing to risk getting banned that's all I can say. Additionally, extra time will be added to your key for the time the bot is down.
There is no way to get yourself unbanned. You can only start a new account. You can try emailing PokemonGo about it. But that's not up to us to getting you unbanned.
We are aware of issues with Gen3 implimentation, the devs are now aware of the situation and will be working to release a patch to help make Gen3 integration smoother. We will announce here once it has been completed.