Definitely do the flush! Even if you get no stones you will take out icky used bile etc. Do an enema afterwards if you can.
Two months is more than long enough to overdose on apple juice and other juices. Take a break. You don't want to turn orange!!! (I did!)
There are herbs you can take that will help too and won't mess up your body Sugar levels. I take a liver detox mix that includes bupluerum and milk thistle, and I ordered a mix from this page to soften the stones: