Run the engine on an auxillary fuel tank suspended above the bike.
That eliminates the carbs.

Next plumb the auxiliary tank into the pump inlet.
Disconnect the line at the carbs.

Put thumb over fuel line end....the pump should stop once pressurised.
Take thumb off...pump should start and spurt fuel out of fuel line.

Rinse and repeat.

I was going to say that

I would say that if the carbs are already full the pump won't do anything until you take some fuel out of them.
Mine only primes until they're full then won't do it again until I've run it for a few seconds.

Quick update,

I have tested the coils, VR, put in fresh plugs and caps. Taken the carbs apart again (floats are now 23mm and air screws at 1 3/4, needle clips are 3 of 5). Clean fuel filter and clean air filter. Carbs balanced. Pump is running more frequently now.

Starts but only after several seconds of trying but doesn't catch straight away and wont take any choke. Once it is running it seems crisp under revs with no hang or hesitation.

Idle is a bit bouncy 1200 - 1500, seems to hunt slowly almost like a misfire. Exup has been removed but this never affected the idle before so it could be the pilot circuit

I also think I may have something slowly draining the battery overnight so that will be another thing to work through. Could be the battery is causing a weak spark at idle.

I have ruled out the battery. Re-filled the fluids and checked the spec gravity and charged. All cells are good and it passes the cranking drop test. Definitely charging within specs and no parasitic drain could be found. If anything it now cranks even better after the lavish attention.

I haven't had a chance to get into the carbs for the pilot circuits but now, having eliminated almost everything else, I am staring accusingly at the air filter. I put a new K&N in recently and I think it's making the mix too lean. If I partially block the air filter intake port with my hand the bike will start and the idle is smooth. Does this sound logical?

Next step is to sacrifice some small living creature to the Gods and hope for divine guidance

No exup
This will mean the exhaust is a bit big for the engine at low revs, just when you're trying to start it. That will drop the back pressure of the pipe and weaken the mixture.
Putting the air jets in to 1.5 turns will try to address the weak mixture but it's not a solution to it. The K+N doesn't make a lot of difference, it's the airbox itself that restricts airflow.
Take it to a dyno and let them sort it out you'll be chasing it for weeks

Cheers Evil, long term jetting will have to be the answer.

Took the carbs off today and cleaned them again paying really close attention to the pilot circuits and it has definitely made a difference. Two of the pilot jet holders were partly restricted. Starts a lot better now and the idle is much smoother, more like it's old self. I have ordered an OEM air filter just to see if it makes any difference low down.

I think in the end it was a combination of restricted pilots and a weakening battery.

Looking on the bright side I learned quite a bit about the electrical system and after going through all this and know that the things I checked are all good.

Knowledge is power.

The real answer is to put the exup back