You mentioned eating apples and apple juice leading up to the flush, but did you have anything containing oil every day? Otherwise it amounts to a juice fast and flushing is not recommended during a fast. In order for the Liver Flush to work, you need some good oils in your daily diet. About 2 tablespoonfuls is enough. Fat-free diet actually creates stones. Some people need to eat at least some oil on the day of the flush as well, and sometimes the more the better, although H. Clark advises against it. We are just all different.
If you do not have sufficient amount of oil in your diet, the liver will not produce enough bile. You need a lot of bile to move things along in the ducts during the flush. Despite getting only a few stones it does not mean it was a waste of time. Just consider it a learning experience, both for you and your liver. Next time it will be that much easier.