Dear Spencer,
Regarding (1), I think that the wave-elevation time-series are not matching between input and output with WaveMod = 5 because you’ve set lower and upper cut-off frequencies of the first-order wave spectrum.
Regarding (3), the dynamic pressure term should not include the static pressure head (which is calculated internally within HydroDyn), nor should it include a correction for atmospheric pressure. For still water, the dynamic pressure would be zero throughout the fluid domain. I’m not sure I understand what you’re saying, but do you get the result you expect when you set the dynamic pressures to zero?
Best regards,