The Daniel K. Inouye Solar Telescope (DKIST) will include facility instruments that perform polarimetric observations of the sun. In order for an instrument to successfully perform these observations its Instrument Controller (IC) software must be able to tightly synchronize the activities of its sub-systems including polarization modulators, cameras, and mechanisms. In this paper we discuss the DKIST control model for synchronizing these sub-systems without the use of hardware trigger lines by using the DKIST Time Reference And Distribution System (TRADS) as a common time base and through sub-system control interfaces that support configuring the timing and cadence of their behavior. The DKIST Polarization Modulator Controller System (PMCS) provides an interface that allows the IC to characterize the rotation of the modulator in terms of a reference time (t0), rate, and start state. The DKIST Virtual Camera (VC) provides a complimentary interface that allows data acquisitions and accumulation sequences to be specified using a reference time (t0), rate, and execution block time slices, which are cumulative offsets from t0. Re-configuration of other instrument mechanisms such as filter, slits, or steering mirrors during the observation is the responsibility of the IC and must be carefully scheduled at known and pre-determined gaps in the VC data acquisition sequence. The DKIST TRADS provides an IEEE-1588-2008 Precision Time Protocol (PTP) service that is used to synchronize the activities of instrument sub-systems. The modulator, camera, and mechanism sub-systems subscribe to this service and can therefore perform their tasks according to a common time base. In this paper we discuss the design of the PMCS, VC, and mechanism control interfaces, and how the IC can use them to configure the behavior of these sub-systems during an observation. We also discuss the interface to TRADS and how it is used as a common time base in each of these sub-systems. We present our preliminary results of the system performance against known instrument use cases.