Sometimes what I will do is let the stone sit in some hot water for a while. Then after I remove it will take my best squirt bottle and start blasting the crack with it.
I have also tried using a sonic cleaner. Never had any luck with it though...
There has been much discussion about crack and pit repairs. How and what to fill them with.
Opticon has it's place. Primarily for cracks. I can't recommend it. Just never had any luck at all with it. For any application....
Maybe someone else can recommend their favorite, but mine is the two part 330 epoxy.
Of course no matter what you decide on trying, the polish has to come out of the crack !
Just for fun, you can do a forum search using search words or phrases like, "how to pits", "how to cracks", "pits cracks", and any other combination of words you can think of. Lots of archived topics should pop up !