I haven't gone back through this entire thread, so I dunno what tests you've done. Apologies if I'm covering old territory.
Yes, SFJOTA is correct - two pickups and two ignition circuits. One for the centre cylinder and one for the outer two cylinders which fire the spark plugs together.
An intermittent fault on one of the circuits (in this case the centre one) could be anywhere in that ignition circuit from where the power supply and earth wires divide to the individual BTZ boxes. So it could be pickup, BTZ ignition box, coil, HT lead, spark plug cap or spark plug, or any of the wiring between them.
Just approach it logically and you'll get there. A handy diagnostic tool is to swap components between ignition circuits and see whether the fault follows a component. Try swapping the BTZ boxes over. If the centre plug fires reliably and the outer two become faulty, there's your diagnosis. You don't have to un-bolt the boxes to swap them, just un-plug the multi-pin connectors and plug them into the other boxes.
Also try swapping spark plugs and plug caps around.
Another handy trick is to start the bike in the dark and have a good look around the coils, HT leads, plug caps and plugs. If you see any arcing, then there's a problem. The high voltage current is tracking on the outside of a component and jumping to earth. Can happen if insulation on the HT leads or plug caps has deteriorated.
It's not possible to swap coils because they're different (one is a double coil and the other is single) but you can test the primary circuit resistance with a multi-meter. Should be 3 to 5 Ohms depending on the type of coil. The high voltage side of the coil has a much higher resistance of several thousand ohms (typically 6,000 - 10,000) but an open circuit reading on the meter is not necessarily definitive. Coils that test as open circuit on the secondary can often still work OK because the high voltage can jump gaps (as it does in the spark plug).
Before pulling the alternator rotor off, check the resistance of the pickups. Again, my memory is a bit hazy, but something like 50 Ohms rings a bell (someone will be able to confirm). Best way to do that is to un-plug the harness from the BTZ boxes and put a meter probe on the pickup wire with the other probe earthed somewhere. Doing it that way will also show up a problem with the pickup wire.
If you end up having to remove the alternator rotor (borrow a puller if you don't have one - I'd lend you mine but there's gotta be someone closer to Cornwall than Tasmania!), there's a range of diagnostic tests you can do.
Firstly, visually check the insulation on the wires to each pickup. You can also check the insulation with a meter. Repeat the pickup resistance test while jiggling the wires a little bit at the pickup end. If you get an intermittent change of resistance, it could indicate poor insulation.
As for swapping pickups (to see if the fault follows a pickup), it's been a while since I looked at an original pickup plate, but if I recall correctly, it's not possible to un-bolt the pickups and swap them over. You can however swap their functions if you feel like a bit more of a fiddle. Mark the position of the 2-lobe rotor on the end of the crank so you can put it back in its original position, loosen the rotor (I think there's a couple of grub screws holding it in place) rotate it 90? and tighten it up again. Then swap the pickup wires at the ignition boxes. The engine will run, but the pickups will be firing the opposite ignition circuits. Note that with a BTZ ignition system you don't need to replace the alternator rotor to start the engine. You can test run it OK with the rotor off. (Earlier HKZ system is different, and won't run with the alternator rotor removed).
That should be enough to keep you busy for a while
