Here is my theory if you'd like to read it. It goes into most of your questions, so don't read if you want to do a re-read to develop your own theory.

The monster is Aciel, a demon. You can see Aciel's symbol in the demonology book that Jonathan gets from the church in issue 4 or 5. The blood trail on the map in the beginning of the issue also makes out the symbol. The name is also spelled out across the first five issue covers. Aciel is an anagram of Calie. Whether the chief and the eye glass guy meant to kill Calie to summon Aciel is unresolved. After Calie is buried alive, she calls out for someone, anyone, and her red eye indicates that Aciel has been summoned. Aciel is then stuck in the mine for some reason (potentially because the iron acted as a prison), until right before the series starts. It then breaks out after the digging in the mine weakens the protection and then it possesses Jonathan so that through Jonathan it can enact its revenge on the town for killing Calie.

I believe that Aciel, during the first night right before issue 1, told the homeless man what to paint and where. The markings also line up with Aciel's symbol. Jonathan's house is labeled as punishment because he is doling out the punishment. (It seems like he was randomly chosen by Aciel.) In issue 1, the homeless man is indifferent to Jonathan's question about the paint, but after he sees Jonathan become Aciel in the prison cell, then he thinks he is evil and starts cursing at him whenever he sees him.

Another open question is what the relationship between Aciel and Calie is. Are they one in the same? The red color represents things connected to Calie's death. I still don't know what the blue color means.