Just looked back through the thread for pics. I have a suggestion.

First, it looks like your buying custom cut plates? If so, order them cut to size, they always come cut slightly oversize, so rather than milling all that away from the edges, you would just be trimming a mm or so off each side saving you in both material costs and machining time.

Second, you could make a fixture plate for accurate location after flipping. Carry on machining out the guts inside on your vice, in the pic below the three holes circled you could drill out .1mm undersize, hand ream them to size, then use dowel pins in these holes to locate into the fixture plate. These dowels will also pretty much hold the part in X and Y, with a bolt through one of the big square holes and a large washer just to keep everything dead still. Then you can profile round the edge and chamfer or radius your top edges. When it comes to do the square hole which you have a bolt through, just have a pause in your toolpath and move the bolt over to a different hole. This would then also give you the ability to pull a case off and put a new one on without having to rezero, you could also run a toolpath on all your cases in a row, saving you the need to keep changing tools. If you have more than a couple of these cases to make, it would be well worth the price of a 10mm slab of ali and the hour or so it takes to draw up, machine and fix in place. And also far preferable to dealing with super glue.

(Ok it won't let me upload a pic for some reason, but there's only three holes I can see so you should get the idea)