How to build a mantel on rough stone fireplace
The first step is to put the hidden fasteners in. Like you said, I would use a rod system and epoxy it into the stone so that they won't come out. 

As far as getting it to sit on a flat plane, I wouldn't chisel the block out. I would build up the area where the mantel will sit with a mortar that is colored to match the stone face. You can pick up mortar tints, like the Quickrete Mortar Tints. Just use a thicker mortar and mask off the areas that you don't want to get covered. Build up in layers if you are laying it thick. Just cover the area that you want the mantle to sit.