There are actually three pulsars....one for each cylinder in one unit. So, it is possible that one might have an internal high resistance short to another. If you do not have the manual, at least check the circuit diagram in the back of the owner's manual and you will see what I mean.
http://cdn.powerequipment.honda.com/marine/pdf/manuals/31ZV7614.pdf
The magnets on the flywheel are energizing the exciter coil, which provides the high voltage to all the coils through the cdi. So, if two cylinders are good, the exciter coil is probably putting out the correct voltage.
Back to the pulsars..... If you do not have the proper tester to measure the outputs (which are very small.... .5v or less), check each lead to ground with an ohm meter...and compare that way. Also measure from pulsar output lead to the other two leads. Those measurements should be the same.
One other thing to check are the timing marks to be sure that the timing belt did not jump a notch.
Mike