To recap, I was having issues with the left cylinder not firing. I swapped coils (left to right) and the right cylinder would not fire. I bought a new set of coils and when I kicked the bike over the left side would only backfire and sputter. I realized I hadn’t changed the plugs and when I pulled them, both were fowled. I put in new spark plugs and the left cylinder didn’t seem to be running. It took a little bit, but it definitely wound up firing, I could tell because of the heat on the left exhaust. Although, the left side was considerably cooler than the right. Took it out for a spin and the bike was really struggling not to die. Had to keep the throttle cracked a bit. As I was driving, on two occasions, when I pulled in the clutch to shift the bike died completely and almost instantly. If I dropped into gear if fired right back up. I just don’t know where to start. Valves, timing, compression, carbs? Can post a video tomorrow of the idle if it helps. Right spark plug showing really heavy signs of being too rich. Left spark plug almost looks brand new.
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Sounds like an ignition problem. Also sounds like it is not running on one cylinder. Check to make sure that the coils are hooked up correctly.
What year and model bike are you working? I would start by checking the ignition timing using a timing light against the rotor LF mark on the clutch side plug, and the F mark on the throttle side plug. From the symptoms you describe ignition might be the primary issue here.
1975 CL360 K1 Scrambler
Did you also check the idle? Could be why it dies when pull clutch, but the ignition/timing is probably the main reason it is not running correctly in both cylinders.
1979 CB 400 T (Cafe Racer)