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As I understand it there is a preferred frame of reference based on the velocity for the CMB and our galaxy is moving in relation to it (at about 600 km/s). I think this is how the Hubble Flow is defined. Given that there are no relativistic effects, and I really mean time dilation, between distant galaxies that are moving apart due only to Cosmological expansion, is there a way to determine a distant galaxy's speed relative to the Hubble Flow by measuring time dilation effects between there and here? If so using that and observed red-shifting, one could establish a more accurate measurement of the Hubble Constant.
No. Time dilation is expected and observed as a result of universal expansion (e.g. in the light curves of type Ia supernovae and the duration of gamma ray bursts, Blondin et al. 2008; Zhang et al. 2013). There is no way of distinguishing between a Doppler shift and cosmological redshift for an individual source.
There's no way to distinguish cosmological redshift from proper-motion redshift because there really is no difference. The universe isn't a smooth FLRW geometry with galaxies moving on it like test particles. It's more like a bunch of Schwarzschild-de Sitter patches stitched together. If you smooth out the bumps, you get an approximate FLRW geometry (increasingly accurate at larger scales), and you can define a scale factor and cosmological redshift formula and so on, but nature doesn't care about such approximations, it just integrates everything numerically. If you knew the exact shape of spacetime, you could compute the exact redshift by parallel transporting the four-velocity of the emitter to our location along the path of the light, then using the special relativistic formula. Computing the redshift as a factor for the emitter's peculiar velocity times a cosmological factor times a factor for our peculiar velocity is just an approximation.