OK, I've got the first of these boards up and running. Anyone who happens to be committing aviation over sunny Cumbria is welcome to listen out for ident 406178 (on the ground)!
Here's how I put the AFF/regulator board together. There'll be other ways that may be just as good or even better but this worked for me.
1. Using the two small header strips, "dry" assemble the ARF and regulator boards. The ARF component side faces away from the regulator board.
2. Turn the assembly upside down and place it on a flat surface. The large IDC connector is taller than the boards, so I sat the board an the edge of my table with the IEC connector over the edge. The objective is to get the ARF board and regulator board tight up against one another with the header pins fully inserted in both boards.
Now solder the pins at the end of each header strip, four in total. Use the minimum amount of solder possible and beware short circuit bridges - the pins are rather close to one-another!
Now gently remove the ARF board and check that the header is fully seated. If not you can resolder the pins whilst pushing the header down.
Solder the remainder of the pins on the regulator board, again being careful to avoid solder bridges.
Put the ARF back in place and carefully align the SMA connector, noting that it won't slide fully home onto the ARF board because the regulator board is about 2mm longer. I used some electrician's tape to hold everything in place.
Gently solder tack the two earth pins on the SMA connector to the lands on either side of the pigtail connector. This will hold the SMA socket in place and you can now remove the ARF from the regulator board and solder the two earth pins and centre pin to their respective lands on the other side of the ARF board
Finally set the ARF fully home onto the header pins on the regulator board and carefully solder all pins on both headers. If necessary, tidy up the solder tacks on this side of the SMA socket.
That's it! Do one more check that you've not inadvertently bridged and connections and that all pins have been soldered properly, then plug into your RPi and apply power. Within a few seconds you should see the green "Heartbeat" light flashing every second on the regulator board, signalling that all is well.
Edit: Corrected first image