Just spam the beginner SP Quests. Usually will get pebbles, but every now and then should get a silver chest that has one of those crystals in it. Was a bit low on those ones as well so was spamming them today.
zzz, too bad you cant downgrade mats in shop: would happily trade tier3 stones for tier2 ones... even if that was 1:1 rate... oh well, time to autofight beginner...