They never checked the farm until 6 days after the abduction. All tracks would have been driven over by then.
How do you know LE never took prints from up by the house?
Perverts are secret in what they do. And boys do not like to talk about things that may be considered to be strange.
Pervs don't have to be going into the showers, but men have to go to the bathroom, so I imagine he did use bathrooms during the day.
We don't know if LE considers he did it. We just know he is a POI. Maybe LE thinks he knows who did it.