I agree with your thinking that the flashlight and the ransom note are linked, but that the flashlight is not linked to the act of killing.
And, yes, no fingerprints, no connection to who handled it. An Intruder who thought along the lines you mentioned would have, in my opinion, taken the flashlight with him.
BOESP,
I agree, an intruder would have taken the flashlight with him, and if we can work that one out, why not the stager, that was my point with the other allegedly missing items e.g. why take those but not the flashlight?
Also if the flashlight was simply placed in a drawer who would be any the wiser?
It was probably used as an aid to writing the ransom note then wiped clean as a precautionary measure?