Hi Dusty;
First, I don't mean to put words in Tin's mouth, but I don't think he was asking "what are you here for" to insinuate that you were in the wrong place. More like what are your interests and such.
I don't really know the capabilities of the Shop Smith, but you say "horizontal boring". You can get the counter bores you want if you are willing to pop for one in 5/8", but that one alone will run about $35. If you can do horizontal boring then you can probably make the counter bores using a flat ended boring bar.
To start your hole, no matter what kind of machine you use, start with a centering drill. It's a short, plain shanked drill bit with very short flutes and a small stiff starting point. Just use it to make a dimple to keep the drill bits from wandering off the position you want to start them. Then continue from there.
From there I would drill through with your bit for 1/4-20 tapping and then drill or bore the next bigger bore you need. By boring you can make a flat bottomed hole.
When you tap aluminum, it can be tapped dry, but it is much easier if you use some kind of tapping aid. I use paraffin wax, rubbed on the tap. One of the few things that WD-40 is good for around machine tools is tapping aluminum, so you might try that too. Clean your hole out often to keep chips from plugging the tap.
I didn't catch how deep you need to go with these holes. If they are fairly shallow, I would drill the smallest hole clear through the piece and then do the larger hole. If they are pretty deep, start with the smallest size and just drill a short way, then do the larger bore. Finish up by completing the smaller hole through. If the hole is not deeper than the full length of the flutes on the drill, just drill the small hole clear through to start with. Clean the drill flutes often by backing out the bit and then going back in, (pecking).
Dean