I don't have any experience with moly coated handgun bullets but shot benchrest rifle for several years. At one time, nearly everyone was using moly bullets in their 6mmPPC benchrest guns. Cleaning was typically done with J-B bore paste and a 50/50 mixture of Kroil's and Shooters Choice (or your favorite solvent). The benchrest shooters stopped using moly when it was found that the moly builds up in the leade of the rifling and can't be removed. I ruined the fine accuracy and required barrel replacement. Not sure how this applies to handgun shooting but I don't use moly anymore.

In rifle shooting, you would have to increase the powder charge to return to the same velocity achieved with non-moly bullets.