It may be quite pitted, then. Unfortunately, the acid in vinegar will most surely harm the stone and discolor it, so too with citrus. It may be a matter of finding different tools, a smaller brush for the more delicate details and for the finer pits.

[He did not address the obvious discomfort, aiming instead for the at least lukewarm acceptance of help.]

Oils too, will discolor it. Though it takes quite a while to do, the best method is but clean water, and gentle soap.