ORAC,
Perhaps I can help a bit here.
You're absolutely right that any change now to the A is going to cost. How much depends on a number of things that none of us are fully sighted on:
1. Your point about structure - removal of the boom receptacle would change a number of structural parts on the upper surface - but the new configuration would be very close to the B model, so it's not all new stuff. Possibly.
2. Software - main change would be to the fuel system management software, moving fuel around the tanks and handling the refuelling flows. Again, moving closer to the B model system.
3. Fuel system hardware would also need changing to add the probe lines and remove the many changes that were required to the system to accept boom refuel rates. Once again, moving closer to the B layout.
4. The least hard part of the job should be installation of the probe itself. The aerodynamic shape of the fuselage forward of the probe is the same for all three variants, as is the location of the cockpit canopy arch. If the space is truly vacant on the A, probe installation should not be a major challenge.
Taking the gun off the Typhoon was a major challenge (I was told) due to the high weight of the gun system and the particular way the aircraft's flight control system works. Your point about the F-35A is well made, although the weight involved is less, and the flight control system is different, and I would expect some software changes to be required.
Best regards as ever to those working the options,
Engines