We investigate the general question of implementing a chiral MSSM like D-brane sector in Type IIB orientifold models with complete moduli stabilisation via F-terms induced by fluxes and space-time instantons, respectively gaugino condensates. The prototype examples are the KKLT and the so-called large volume compactifications. We show that the ansatz of first stabilising all moduli via F-terms and then introducing the Standard Model module is misleading, as a chiral sector notoriously influences the structure of non-perturbative effects and induces a D-term potential. Focusing for concreteness on the large volume scenario, we work out the geometry of the swiss-cheese type Calabi-Yau manifold IP [1,3,3,3,5] [15] (3,75) and analyse whether controllable and phenomenologically acceptable Kähler moduli stabilisation can occur by the combination of F-and D-terms.