If you attach a logistic chassis with an extractor module (either mark 1 or 2) to the side of the furnace it will extract any excess products from the furnace and send them to the default route, do not worry about the extractor module taking items that the crafting pipe was waiting for as it has a lower priority so will not take the items unless no other pipe wants it.

In general, look for custom brushes that you can use to vary your height map/terrain levels to help keep them from being too smooth (google image search heightmap and search through varients like islands, rivers, mountains to find things to use as brushes, or just google search world painter brushes and download ones you like to try them).

In order to get the "rough" areas like you are asking for, find small height maps with high, interspersed contrast. You could technically do this like 2xedo said with a noise brush. The black/gray/white contrast tells world painter how much an area should be changed compared to the next pixel over on the height map. Try shrinking the brush size to cover a smallish area of the map, add some height, move the cursor slightly, then remove some height to dig back into the earth a bit.

Then try out making custom terrain (percentages of stone/cobble/gravel/sand/red sand/dirt - it looks like you were already on top of this with the stone/cobble mix) for cliffier areas in order to add more interest/variety to the landscape.

If you haven't watched Lord Dakr's world painter tutorial videos on youtube, I would suggest you do that. The link here goes to his first tutorial video at the time stamp that he starts talking about custom brushes (10:11). At 13:40 he starts making his demo map, explaining some of the problems that can come with the default brushes, including the problems of not looking realistic, which seems to be your issue.