I have a bit more time now so a longer explanation.
A friend's Yellow Peril replica. We were using rollers to start it so the engine was spinning up fine. No matter what we did only one side, always the same side, would run. Just like yours
The bike was wired exactly as per Pazon instructions. Sorry I don't know the exact Pazon unit but it wasn't the cheapest one nor the most expensive one.
Spark at both plugs when tested. But on a wasted spark system!!!! This is important.
Your message looks like a photocopy of what we did plus we're did a bit more as follows.
New plugs. BP7ES. Used 5 k resister plug caps. Wire cored HT leads
Swapped leads to other side
Went through the wiring with a multimeter testing every single connection. Giving them a good pull to check any break inside. I learnt the Boyer hidden broken wire in the trigger unit trick 10 years ago.
Disconnected the feed side to the ignition and just ran a wire straight from the battery to ignition bypassing all switches
Tested and swapped out coils. Standard coils with standard mounting.
Tested and swapped out leads and caps
Fitted new spare carbs. Checked fuel lines filters tank breathing etc. New gas.
Sent Pazon unit to Pazon for testing. We are in NZ so very easy.
Checked compression
Took rocker covers off and checked valve clearances and visual checked as close as able valve lift timing
Still nothing.
But then I talked further with my friend and realised that while he sent the black box to Pazon for testing he did NOT send the trigger plate.
Fitted a new trigger plate and checked rotor clearance.
Instantly started both cylinders.
We were fooled by the spark at both plugs. But we were seeing the wasted spark on the bad cylinder side.
And when we swapped the plugs over it made no difference because what had previously been the wasted spark on the non firing cylinder became the correct firing spark on the good cylinder. It also explained the occasional popping on the bad cylinder side. The wasted spark was firing the unused fuel in the cylinder and firing it out the exhaust.
You have checked and swapped pretty much everything as we did. But I bet one side of the trigger unit or associated rotor is your problem.
Just because you see a spark at a plug it doesn't mean it's there at the correct time.



A couple of the other guys have also suggested this but I have detailed our tale of woe because it so closely matches your experience.