After a long delay (other work, life getting in the way, general laziness etc) I ran some more tests on the Pibox. With the fans disconnected (actually, one disconnected itself!) and the case assembled I’ve been running the box to see how bad the temperatures get. With two of the three Pi cards operating, and all 3 powered up, pi-star, which is on top due to the DVMEGA hat settles at 60 degrees C, and the utility Pi which has a Discone attached settles at 50. So not actually bad. I think what I will do is go back to Plan C or whatever it was and run the fans via a transistor hanging off the GPIO port of one of the cards so the fan comes on if it is getting a bit steamy. For now, at least it means I can run pi-star 24/7 again, especially as I had to upgrade it by hand as it has missed a lot of the overnight updates.
And it saves me having to run mains power into the loft.