Two-dimensional (2D) transition metal dichalcogenides (TMDs), like MoS2, have unique electronic and optical properties, which can further be tuned using ion bombardment and post-synthesis ion-beam mediated methods combined with exposure of the irradiated sample to precursor gases. The optimization of these techniques requires a complete understanding of the response of 2D TMDs to ion irradiation, which is affected by the reduced dimensionality of the system. By combining analytical potential molecular dynamics with first-principles calculations, we study the production of defects in free-standing MoS2 sheets under noble gas ion irradiation for a wide range of ion energies when nuclear stopping dominates, and assess the probabilities for different defects to appear. We show that depending on the incident angle, ion type and energy, sulfur atoms can be sputtered away predominantly from the top or bottom layers, creating unique opportunities for engineering mixed MoSX compounds where X are chemical elements from group V or VII. We study the electronic structure of such systems, demonstrate that they can be metals, and finally discuss how metal/semiconductor/metal junctions, which exhibit negative differential resistance, can be designed using focused ion beams combined with the exposure of the system to fluorine.