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The power wire for the CDI does not pass through your regulator/rectifier. The R/R has nothing to with spark. Gradual loss of spark usually points to the pickup coil just above your flywheel. Should be a blue or blue/white wire from your stator. Voltage should be about .5v to 1.0v. An anomaly with the pickup coil is that after a few firings or when they get warm from running...they lose voltage because the coil is faulty or stator voltage to them is irregular or too low.. This means your CDI may not be firing at the proper time i.e. late, at which time some of the current in CDI's capacitor has bled off giving you a weak spark. So get out your multimeter and check the pickup coil voltage.
Glenn
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