The main cause of the misalignment at the first attempt was the result of flipping the stock over half way through because of said crash. That and the fact that the stock width that was defined in the CAD / CAM wasn't quite right.
This time round, I was careful to double check that the tool lengths etc were spot on - by jogging to Z10 in G54 with each tool loaded (G43 T13 H13 etc) and checking that a 10mm ground drill shank would just about fit between the tool and the work surface.
I made certain the Martest (Haimer clone) was set up and used it to touch off on the back edge and top surface of the stock. All looked good.
Finally, I managed to connect up a cheap (£20) and nasty retracting air hose I got from Lidl this week using a 3-way airhose adaptor, also from Lidl for £5. I have some air tools from the Wavedriver days, including a couple of nozzles. So now I can blow swarf clear if it starts to build up in a way that looks hazardous to the tool.
With all the tools set up and the (slightly rejigged) programs on the USB stick, progress was quick. The total machining time is only 12 minutes (plus tool changes etc), so the whole job took me around 20 mins or so.
Milling out the middle fixing pockets:
Job done! Not 100% perfect, but then I don't imagine anything ever will be. But certainly good enough for the likes of me.
Now to move on to the X axis stuff...