Just realized I missed your reply with the PDF (either because I was posting when you submit it or because I am oblivious... I'd bet on door number two...)
The sketch you put up is maybe possible with the nomad as sketched. The through holes are not possible. The well might be, but it is at the limit, and I would need to try to see if it is. There is a little more than the 3" (76.2mm) spec for the Z axis, but not much. I have done 80 mm (40mm material and 40mm tool extension), but it was dead tight. Your sketch shows 3.5" to clear the top edge (you MUST have clearance or there is no way to set zero and to zero for tool length) which is 89mm total. I don't know, and am not in position to check right now, if there is 9 more mm than I have squeezed out of the machine.
If modification of the design is possible (well depth, at the edge in particular), then you should be in. If not, I'd want to get on a machine to try it first.
As it sits, the order I would use (others might go a different order) would be drill the through holes first on a drill press, as the most likely to mess up operation, then machine the well and tap drill or tap bore (the bore is about 0.150" for 75%, or 0.162" for 50% thread) for the 10-24 holes in the first fixturing, then reset the part and bore the opening in the end through and cut the seat for the O-ring. The tapping is not practical on the nomad. Do it by hand. I would pop the $100 for a hand tapper to make it easy, if I was doing more than a couple, rather than do it with a tap wrench.
The bore for 10-24 is practical with a 1/8" (0.125") tool, but would be better done with either a 3/32" (0.93") tool as a bore, or drilled. The nomad can drill, but it is easiest using 1/8" or 1/4" shank drills (often seen as circuit board drills), rather than standard drills. I would use a 3/32 diameter center cutting flat endmill, myself, with a helical entry to full depth leaving 0.1mm (0.004") for a finish pass. The target thread, for me, would be 60% in acrylic, and 70 to 75% or PTFE or HDPE.