Faulty pick up coils?

Ok, sorry for the delay in reporting back but life in general and fishing in particular got in the way  
I’ve read your explanation of how the coil set up on the bike works and it makes sense to me so I’m ok with that now. 
I’ve  just done your test and found that all three coils will jump 10mm from one HT lead to its partner on the same coil so presumably that means the coils and pick ups are healthy? 
I await your next instruction oh mighty Jedi master 

Next I would hook up all the primary wires and do the same test while cranking the bike over and see what happens. Maybe what your experiencing is a significant drop in battery voltage during cranking and that's what's causing your problem. So do the test and monitor the battery voltage during cranking. if it drops below 9 volts, either the starter is drawing too much amps or the battery is weak, but let's see what happens next.

Which begs me to ask, what is the present problem you're fighting your way through???

Ok me being me I’ve jumped the gun a bit 
instead of doing the test as in the manual, I misunderstood (didn’t read) your instructions properly and I tested them on the bike using the starter motor to spin the engine over. So the results are with the starter drawing current. I’ve got a power socket in the tool tray/airbox lid under the seat that has a digital voltmeter built in. With everything switched off it reads 12.7v but I didn’t check it while cranking the engine, I’ll check that today and report back. 
The problem I’m trying to cure is the engine is very difficult to start (it was instant after scotches carb mod) and it runs very rough from tickover right through the rev range and it stalls very easily then refuses to start. 

Waiting to hear what the voltage is during cranking (with the sparkplugs in) but in the meantime, your statement " The problem I’m trying to cure is the engine is very difficult to start (it was instant after scotches carb mod) and it runs very rough from tickover right through the rev range and it stalls very easily then refuses to start. " makes me ask 

Did you check the basic ignition timing and advanced ignition timing at 2000 rpm?

I have checked the ignition timing in the past but it’s really difficult to do while the motor is running so roughly? I’ll try again later on today and report back with the results and cranking voltage. What I can’t understand is why it was running so good for a few hundred miles and then started playing up? 
if I didn’t know 100% that the carbs where spotless I would say it was a dirty carb problem?

Ok, another hour in the garage and I’ve possibly found the problem. The voltage drops to around 10v when cranking with the plugs in so that seems to be in the ball park ruling a duff battery out. I managed to get her started and running voltage is 13.5v so hopefully the charging system is good? However while trying to check the timing I couldn’t get my trusty Gunsons strobe light to work properly, it was working intermittently flashing in spurts then nothing then flashing again so I couldn’t check the timing. The not flashing bit only lasted a second then it would be ok for a couple of seconds then it would stop again? As it’s always worked perfectly before I thought I would try it on my other bike a Suzuki T500 twin where lo and behold it works perfectly? So although I haven’t got a clue what’s causing it I’m certain I’ve got an ignition issue now. Maybe the igniter unit is breaking down?
over to you oh mighty Jedi