I made some more progress on the aluminum showpiece I'm working on and got the somewhat difficult areas complete.
I was able to flip the bar of parts over and faced it all down till each of the parts where separated, I released the vice a little and tapped each one down to ensure everything was perfectly flat to the bed of the minimill. From there I was able to set up a mini hard stop that attached to the top of the hard-jaws and placed a parallel down to raise the part from the bottom and used an edge finder to find the back right corner of the 2" square block and used that as my work zero for each of the sides.
I ended up using a piece of ABS plastic to clamp against the domed face (see the previous post) to prevent the steel hard-jaws from ruining the finish.
For the actual side milling operations, I ran into an issue where the blending of the finish from the first operation wouldn't quite match up and so I had to shave it down to blend it all in manually with a small file. All the marks will be cleaned up and hidden after they get tumbled. I was using a twenty thou ball endmill (0.02") with a one thou stepover to finish all the small features. I had to use such a small endmill to get as much of the detail on the part as I could due to the way it was designed.