Sorry for the delay finishing up post. Warmed up tractor for about 30 minutes before doing all this. Replaced set screw with same size fine thread hex. Easy access to loosen now, just no room to get a phillips on the original. Turned separator fill to off. So removed separator, red float ring and spring and o-ring and element. Used a rubber strap wrench to loosen bowl retaining ring. Cleaned bowl of gunk and debris. Installed new element and lightly lubricated new o-ring with engine assembly grease. Dropped spring and red float ring back into bowl. Filtered a small bottles worth of diesel with a filler neck strainer and filled bowl almost to top. Carefully mated bowl back to housing, excess diesel went into bucket. I was hoping that the overflow during this part would ensure the bowl was filled. Tightened everything up, opened separator fill and tightened set screw (bolt now), checked for leaks started tractor at about 2300 RPM. No hesitation, stuttering or anything. No issues now after about 20 hrs. As previous owner has changed fuel filter approximately 120 hours before, and the gunk was not in separator when I purchased, I did not change fuel filter. I attributed the gunk in the separator to my treating the fuel and possibly cleaning out the system. The element in the water separator is a quite fine mesh. It is a strong first line defense from the tanks to stop debris from getting in system.
So no bleeding necessary in this case, fuel filter replacement will indeed require bleeding as filter is oriented 180 degrees opposite separator - no pre-filling possible. Hope this may be of use to someone.