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...any change when pulling the choke when the bike is slowing? would be somewhat a test for supply in the bowls themselves... floats hung up.. less likely, needles stuck which is more common for rubber-tipped than these..I rode the rest of the way home with the petcock in Prime mode but the engine died a few times along the way.

after I found someone had grinded down the lobes of my advance mechanism
yes and the kill switch too....but if it's not electrical, you are going to have to go back to gas supply.. ...any change when pulling the choke when the bike is slowing? would be somewhat a test for supply in the bowls themselves... floats hung up.. less likely, needles stuck which is more common for rubber-tipped than these..
I am guessing this is your setup then? Perhaps you got a defective kit-it's possible. and they have a note per wanting suppression plug caps too. So you might want to clean those up if they are the originals and/or get plugs that have suppression...The suppression stuff is part of the secondary's impedance and might affect heating at the coils if that were a thought...
..if the coil is getting hot unless you can get one of those battery operated indoor/outdoor thermometers. The sensor would be on the coils or any thermom that saved Highest temppp...might do. ie part of the "always check the last thing you did" Especially so if the bike was running properly before you did it...but did it ever?
I'm wondering why you chose to eliminate one of the coils?
One of the reasons that Suzuki uses two coils is to give the coil sufficient time to recover. The faster the RPM the less time there is.
If you have one coil it has to run twice as fast which means it is not likely to fully magnetize the coil when the ignition is fired. It could be also causing the coil to get hotter than normal and further reduce its output.
I would go back to two stock coils and wire as per the manual. See if that keeps it from stalling.
Ok..but...how about the spark plug caps> using the old ones? Coils are not meant to run straight to the spark plug unless it's a lawn mower...You are aware that the original plug caps had 5000 ohm resistors in them? If you are running just straight copper with a different kind of cap without this xtra impedance....? II switched them out with 7mm Dynatek Copper plug wires.
My reasoning here is that no matter if you have one or two coils they both will always be working twice as fast so there shouldn't be any difference between having one or two. Am I misunderstanding how the system is working?
Okay, I’m trying to follow along here.It basically gets down to this. A four-cylinder engine is two 2 cylinder engines. The main complication is how they are fired. A 4 cylinder fires twice every revolution of the crank. but because of wasted spark, there are actually double sparks going out (i.e. 1-4 or 2-3) A 2 cylinder also fires twice per crank revolution and it is also wasted spark.
.
Now I’m not familiar with this 2 cylinder engine you speak of, but I have had a Honda 305 Dream with a twin cylinder where both pistons move up and down together ( so it could use a wasted spark system in theory) and I have had a Honda 305 Super Sport twin where the pistons move up and down opposite of each other ( think John Deere Johnny popper style) and have unequal firing pulses, which would not support a wasted spark ignition system because of the uneven firing impulses.
So which style twin are we talking about?

...because it has two pickups on the crank and therefore the black box is going to get a signal every 180 degrees...it'd have to be pretty tricky circuit to figure out how to stop firing the coils for the "correct" 540 degrees ...yes it looks like the EIS is sparking during the 540? between positions two and five. However, I think this is just how the EIS was designed
...because it has two pickups on the crank and therefore the black box is going to get a signal every 180 degrees...it'd have to be pretty tricky circuit to figure out how to stop firing the coils for the "correct" 540 degrees ...
but I'm hoping you found the easy and correct fix at the ignition or kill switch.