What exact spark plugs do you have?
Tested Spark plug boots with a multimeter.
Boot 1= 11.9
Boot 2= 10
Boot 3= 10.7
Boot 4= 10
Get new plug caps. NGK 5k ohm. They're a couple bucks each from any automotive store or online. Your numbers are double what they should be, but weirdly all fairly uniform. I wonder if you have 10k ohm plug caps.
Next i tested the spark plug wires.
Wire 1 and 4= 15.7
Wire 2 and 3= 12.9
These might be fine, a normal value would be something like 14.5 or so.
Next i try and tested the actual Coils but it got a little weird.
Coil for yellow and black/white wire= 10.7
Coil for blue and black/white wire= 0.00
I should mention when i tested the coils that the kill switch was in the run position with the key out of the bike.
When i tried the test again with the kill switch in the off position i got no numbers everything was a 0.00
Do you have Dyna coils? If so, it might say the ohm rating on it. I didn't think the killswitch would affect the test, but maybe I'm wrong. Either way, it looks like your 1-4 coil is bad. The blue wire connects to the 1-4 coil.
Saw your other post and do the test that the other member said. You could instead swap the blue and yellow wires from the coils. So the 2-3 coil now fires the 1-4 plugs and vice versa. If the problem is now with the 2-3 then the coil is bad. If the problem stays with 1-4, then the problem is before the coils and likely it's the Dyna ignition. Make sense?
Please also finish the 3k tune up. Cam chain, tappet clearance, (doesn't seem like you can do timing yet) but all these in the 3k tune up could magnify your symptoms.
Looks like we're getting somewhere