Monte Carlo simulation of radiation transport is a scientific instrument by its own right. Cultivating the skill and the art is no less than gaining mastery in instrumentation. Monte Carlo is never a plug-and-play software tool. Sadly, Monte Carlo is often abused as a black box. Throughout the years I have also been 'offered' co-authorship of to-be papers which were to become publishable if I ran Monte Carlo for them. No, Monte Carlo cannot make an otherwise unpublishable work publishable.
A piece of study begins with a study or experimental design, considering the choice of samples and the control of variables. Letting all variables lose is not going to lead us to anything conclusive.
Embarking on a Monte Carlo project, I would think of the experimental setup the similar way as I would do when setting up a physical experiment in the radiation laboratory. The difference is that now: