If I remember right, both plugs fire at the same time. Maybe you can extend one of the wires so you can reroute and switch them to see if it makes a difference.
I went to heck and back trying to get an M18 in my 1811 run correctly. The final answer was to put an adjustable jet carb on it. I checked compression, swapped wires, changed ignition coil, New pistons and valve job, used a temp gun to see if one cylinder was hotter than the other---but an adjustable jet carb made the biggest difference.
This is a LONG thread but a LOT of knowledgeable folks chimed in with suggestions and helped me think this one through. I suggest glancing through as a lot of good information was posted by fellow OCC members.
http://www.onlycubcadets.net/forum/s...ad.php?t=47254