I have some experience with setting this system up. I'm not at this point sure exactly what goes wrong, but I would advise you first of all to consider if you really want AA stacking in the graphene. Normally, graphene has ABABAB stacking, but in that case you need a bit bigger unitcell in the XY plane, as in the attached example.
I also recall that this is a very hard system to converge. Maybe the parameters used in the attached script helps you a bit!
I had a neat little tool for setting the geometry up, based on some simple parameters (number of screening layers, etc), but I can't find it... I will look for it!