A few comments
Roaming the cage was probably searching out the prey source she could smell.
Bumping is really very common. My snakes will sometimes come right up on a rat and almost seem to rub it or bump it. It's like they are making sure this is exactly what they think it is. It isn't too unusual for the rat to cower in a corner either. They seem to go into a near sleep state. I think the rat is trying to make itself as small and quiet as possible to avoid attack. Others will run like mad.
I use newsprint and / or paper towels to avoid the substrate into the mouth thing. In fact this is what got me to change from eco earth to paper towels. I had a snake strike and get a mouth full of substrate and then it didn't want to eat.
Since eating can be a problem for Ball Pythons I decided it wasn't going to be an issue because of the substrate and I switched.
singingtothesnakes 
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