In atomic layer-by-layer molecular beam epitaxy of high T(c) superconducting films, the chemical reaction coordinate of each molecular layer is monitored and controlled during growth. Distinct synthesis routes are characterized by different intermediate states representing different degrees of order or disorder during monolayer growth. Individual molecular layers with bulk-like superconductive properties can be grown and stacked together with molecular layers having other electronic properties. Trilayer junctions have been grown with single molecular barrier layers of metastable compounds such as Bi2Sr2Can-1CunO2n+4, where n ranged from 5-11, and the electronic properties of such barrier layers have been modified by doping. By engineering the transport properties of the barrier layer, tuning over three orders of magnitude in critical current density has been obtained with approximately constant I(c)R(n) voltage.