Software design requirements for CNC drill machine

Robot Steve's late entry into the BuildBrighton CNC Drilling Machine competition has in some ways spurred us on and in others caused things to grind to a halt. In some ways, seeing such a simple, usable design has us wondering whether it's worth continuing with our little laser-cut caddy. The main difference between our approach and Matt's CNC monster was simply scale and cost:

Matt came up with a solid (though possibly over-engineered) design using linear bearings, rods and bolts by the bucketload, expensive steppers and belts - basically blowing the budget to create the best CNC type machine he could manage.
We stuck to the cheap-as-possible, easy to replicate route, but possibly at the cost of accuracy (we still don't know if our design will actually create a working, functional CNC machine!)

Steve's design fits nicely in the middle.
With 3d printed parts, built from a 3d CAD-based design, he can see his prototype working (virtually) before cutting or casting a single piece of plastic! Yet with minimum part count and easy push-fit construction, there's no need to worry about bolting plastics edge-to-edge and trying to get everything square. It's a great design.

So is it worth continuing with a slightly shonky design, knowing that eventually we'll probably adopt another in the near future? We'll leave that question, and spend our time constructively on the one aspect that no-one seems to have addressed just yet: software.

The budget allows for the complete build - including driver board/electronics and controlling software.
The easiest approach would be to get a MACH3 compatible driver board, hook up the steppers and run everything through some milling software like MACH3. But this is an expensive way of going about things, so we reckon custom software is the way to go.

Also, we're not drilling or milling blank material. Our PCBs with either already be etched, or have tracks and traces already marked on them, ready for etching. So before we start any drilling, we have to make sure our boards are perfectly lined up to begin with.

In something like mach3 we could do this by moving the drill head to a known position and placing the board underneath it, then moving the head to a second (known) position and rotating the board until this second point fits under the head. With the board in place, we could lock it down and start the cnc running.
MACH3 also has a myriad of settings, belt-tooth size, leadscrew adjustment values - all things which make it quite complicated and daunting to the untrained user. For our software we want:

• Minimum settings screens - we don't care how big your stepper motor is, the tooth pitch, degrees per step and so on. The software should work with a wide range of machines without any complicated maths/physics calculations!

• Auto-alignment - placing a PCB exactly squarely on the cutting bed is going to be difficult enough. Cutting the sides square is hard - knowing that you've placed one edge exactly squarely can be hit-and-miss, and if your edges aren't exactly true and straight, getting the whole thing to line up is almost impossible!

• Auto-scaling for different measurement units - NC drill files are commonly described in imperial (inches) but there is software that uses (and an NC drill command for using) metric (millimetres). The software should be able to handle mm and inches without the need to re-calculate the drill position data in the NC drill file.

We're not worried about making everything open source, complying with GNU licences and all that - we're just looking to create some software that just works (in Windows at least) using whichever tools do the job. Of course, details of how the software is created will be explained, should anyone wish to re-create their own, but we're not ruling out any specific technologies just because it's not "open source" or GNU-a-like or anything like that!