I myself have not found any, and I'm pretty sure that Pokétransfer will not allow items to transfer, so are those single-use move boosting gems gone completely?
Most of them are gone. The only one available is the Normal Gem, which can be obtained from dowsing in the lower part of Terminus Cave.
Source: Here and here.
No they're not.
Source: Experience and Bulbapedia
No. They're still here. mostly Invisible items(actually I think Consistently) So have fun exploring caves and stuff with ur Dowsing Machine. And remember to have surf and rock smash!