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- Final Time. Yes you are interpreting final time correctly. Technically, the model should be run for as long as the residence time of your system, but you should find that the number of days in your simulation will not influence water temperature results as these converge on a single day (note: there are some other variables in the model like benthic algae that take many days to reach steady state)
-Model Initial Conditions. These are user specified and are required to support the backward/upstream difference solution scheme (this is the numerical technique for solving for the water temperature for a given element based on the upstream conditions and associated sources/sinks in the element next downstream element). For hydraulics, the volume of each element is computed first under assumed steady state uniform flow hydraulics (using the flow in the headwater boundary condition tab and reach worksheet), and then the governing equation for heat (e.g., Equation 26 in the model documentation) is applied. Due to the steady hydraulics, the volume is constant throughout the simulation for each element and water temperature is Initialized in all elements as headwater boundary condition and computed based on heat source/sinks in each element.
Necessary boundary conditions therefore include: the diurnal variation of incoming temperature at the upstream end of the simulated reach (in the Headwater tab), and conditions at the air/water boundary (e.g., air temperature, dewpoint temperature, wind speed, cloud cover, and shade - along with some atmospheric and evaporation information in the Light and Heat tab), and sediment boundary conditions.
Hope that helps,