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Ok, I just rebuilt the carbs on my '78 CB400T and one side seems as though it runs well and the other side doesn't seem to fire at idle and at 25% throttle and up the side that didn't seem to fire, starts popping and I get an occasional fireball out the pipe. I checked the coil and the rectifier both of which are working fine and I put in new plugs in before the test and then swithced them to make sure it wasn't a bad plug. Any ideas? Thanks.

Maybe a valve issue? I think I'd do a compression test now. That might help steer you toward a solution.

It sounds like a bad exhaust valve to me as well. Do as Poopy suggested and do a compression test, I bet you'll find the backfire side is pretty low.

It's a good place to start, anyways.