It's possible and planned for some of the updated logic the bot will have. Before better stuck detection could be added, we needed to add a way to determine what the client was doing and be able to track it. That was added, so we just need to make the tracking system. A lot of the stuck issues should be fixed with the new movement logic being worked into the bot, so you should expect the bot to hopefully get stuck less. Due to the nature of the game though, and how desync affects us, there still might be stuck issues in the future, but know of the problems and can code around them now.
Making a new instance after not killing mobs after a certain time is not a good idea. It's impossible to eliminate back tracking, and if you need to get through an area to get to the next, you can cause the bot to fail, which is something that currently happens with user plugins that chicken out. We are working on changing the way the exploration logic works to hopefully avoid that.
There's experimental support for % cleared right now, but it's not in the GUI. It's in the grind bot settings file. You can exit the bot, change that setting, start it up, and I think it should work. You should be able to find that file in the settings folder under your league and character name.
With all this said though, one important thing to keep in mind is that you don't want the bot to be too efficient. A lot of people want better, and we'll certainly improve things, but in a game like this, where the developers are actively monitoring what is going on, you're just going to see more bans and detections on the server side if you run the bot at high efficiency for extended amount of times. Generating a lot of instances is not a good idea right now, so be careful with how you configure the bot so you don't look like a bot even more.