1. A method of operating a monolayer deposition (MLD) processing system comprising: positioning a plurality of wafers in a spaced stack in a process chamber comprising a multi-orifice injection system having a plurality of injectors spaced along the spaced stack for distributing gas flow throughout the chamber and between the plurality of wafers; performing a first precursor process by injecting a first precursor-containing gas through the multi-orifice injection system to create a plurality of first precursor gas flows therefrom, wherein the first precursor process is controlled by a first process recipe having a first set of intelligent time-varying set points, the first set of intelligent time-varying set points establishing at least a first flow rate for the plurality of first precursor gas flows during a first time period and a second flow rate for the plurality of first precursor gas flows during a second time period, wherein the plurality of first precursor gas flows is continuous from the first time period through at least the second time period, and wherein the at least first and second flow rates are different; performing a first purge process, wherein the first purge process is controlled by a second process recipe having a second set of intelligent time-varying set points; performing a second precursor process by injecting a second precursor-containing gas through the multi-orifice injection system to create a plurality of second precursor gas flows therefrom, wherein the second precursor process is controlled by a third process recipe having a third set of intelligent time-varying set points, the third set of intelligent time-varying set points establishing at least one of a third time-varying flow rate for the plurality of second precursor gas flows during a third time period or a fourth time-varying flow rate for the plurality of second precursor gas flows during a fourth time period, wherein the plurality of second precursor gas flows is continuous from the third time period through at least the fourth time period, and wherein the at least third and fourth flow rates are different; performing a second purge process, wherein the second purge process is controlled by a fourth process recipe having a fourth set of intelligent time-varying set points; and repeating the performing steps until a film having a desired thickness is deposited on the plurality of wafers, wherein performing the first precursor process further comprises: creating a first dynamic model for the first precursor process, the first dynamic model having first model components (M 1 , M 2 , M 3 , and M 4 ), first control inputs (U), first disturbance inputs (D), first regulated outputs (Z), and first measured outputs (Y), and having a model structure comprising: Z=M 1 U+M 3 D and Y=M 2 U+M 4 D, wherein the first control inputs (U) comprise the first time-varying flow rate for the plurality of first precursor gas flows, the second time-varying flow rate for the plurality of first precursor gas flows, a first flow time, a first precursor concentration, a first precursor type, a first chemisorption rate, a first reaction rate, a first pressure, or a first temperature, and any combination thereof; wherein the first disturbance inputs (D) comprise first process drift, first chamber contamination, or first wafer temperature differences, or any combination thereof; wherein the first measured outputs (Y) comprise incoming wafer temperature, incoming wafer composition, incoming wafer thickness, incoming wafer uniformity, output flow rate, precursor concentration at chamber output, precursor layer composition, or precursor layer uniformity, or any combination thereof; and wherein the first regulated outputs (Z) comprise one or more virtual sensors for determining a first precursor concentration level, a first precursor concentration uniformity value, a first saturation state value, or a first saturation state uniformity value, or any combination thereof.