Should I use the intact rock modulus of elasticity or the modulus of the rock mass?

It really depends on the model and what you are modeling. If you are doing a simple continuum model of a rock mass, without discrete joints, then the modulus is the rock mass modulus. If you are doing a model in which a joint network has been defined using discrete joint, then the modulus is representative of the material between the joints. If the material is intact rock, then the modulus is for intact rock.