We present theoretical and experimental progress towards a new approach for the precision spectroscopy, coherent manipulation and state-to-state chemistry of single isolated molecular ions in the gas phase. Our method consists of a molecular beam for creating packets of rotationally cold neutrals from which a single molecule is state-selectively ionized and trapped inside a radiofrequency ion trap. In addition to the molecular ion, a single co-trapped atomic ion is used to cool the molecular external degrees of freedom to the ground state of the trap and to detect the molecular state using state-selective coherent motional excitation from a modulated optical-dipole force acting on the molecule. We present a detailed discussion and theoretical characterization of the present approach. We simulate the molecular signal experimentally using a single atomic ion indicating that different rovibronic molecular states can be resolved and individually detected with our method. The present approach for the coherent control and non-destructive detection of the quantum state of a single molecular ion opens up new perspectives for precision spectroscopies relevant for, e.g., tests of fundamental physical theories and the development of new types of clocks based on molecular vibrational transitions. It will also enable the observation and control of chemical reactions of single particles on the quantum level. While focusing on N + 2 as a prototypical example in the present work, our method is applicable to a wide range of diatomic and polyatomic molecules.