As of the now the bike starts, maintains a charge on the battery, and idles just fine. In idle though it doesn't seem to want to push past 5k or so revs. In attempting to diagnose this we noticed that when we removed the spark plug cap from the farthest right cylinder (fourth), there was no change to RPMs or to the way the bike ran at all...as if it's not firing. But it has gas, and there is definitely spark to the plug. We tried swapping coil wires to make sure it wasn't a faulty coil and it still didn't fire. He had noticed there was low voltage coming from one of the coils so we had rigged a relay as per the " Coil Relay Modification " on Bikecliff's site. The coils are now getting full voltage.
Other than this cylinder not really seeming to fire I can tell that the right exhaust pipe that comes from cylinder 4 has less pressure coming through the pipe than the other side. I'm assuming that's BECAUSE the cylinder isn't acting as it should, but perhaps there's something obstructing the path of the exhaust?
The odd thing is when the airbox comes off, it runs like a dream. That would then point to a carb/mixture problem but after fiddling with all the carb's mixtures, and putting the airbox back on, it fails to maintain that fourth cylinder firing.
We're kinda stumped. I appreciate any help you guys can give.
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