As far as I can tell that coil is single fire. MM systems use single fire coils. You can't swap plug wires.

I would check the primary wires with a test light while cranking. Check both front and rear. You should be both sides stay on but go out periodically.

 

You sure you are getting fuel? Is the rear plug wet? Look under the nosecone, and see if there is any brown goo dripping from there. This is usually a symptom of a failing cam position sensor. Check the connector located under the right side of the lower frame by the rear brake line to ensure that one has not come out of place, or they are corroded/ dirty. Behind the right side cover by the ECM is the crank position sensor connector. It is barrel shaped. Take it apart, inspect the pins are making good contact, clean it up, and reconnect it. You may also want to check for an intake leak. Do you have the service manual for the bike? If you do there are flowcharts in there to help diagnose problems.

 

 

If the rear primary wire is low most of the time, you need to look for a short to ground in the primary wire or possibly a bad ECU. Make sure power going to the coil is good. Primary windings should typically sit at battery voltage except for short periods before spark is generated.

I would check primary resistance on both coils. Front and rear should be close. If both are off chance are that the coils were damaged by the short.

 

Also with the ignition off and the coil disconnected, measure the resistance to ground of each primary connection, DVM black wire to ground.Red wire to connector.

 

how many primary terminals are on your coil?
2 or 3
if you only have 2 you have a dual fire coil, if so, one will get 12 volts at key/ign on, take a test light, hook it up to the POSITIVE + battery terminal, touch it to ground an make sure that it lights, after that touch it to the other coil primary terminal(not the one with 12 volts at key on). then crank the bike, while holding the test light on that termianl it should flash, this will tell you that you are getting the trigger from the module.
if your coil has 3 or more terminals on it, it is single fire, the same test applies, just that you touch the test light to the 2 TWO triggers, one for front and one for rear, if you get the trigger signal one one, but no spark, it's a bad coil, if you dont get the trigger signal its a bad wire, connection, or module issue.
post up a picture of your coil!!!
m

 

I just so happend to come into possession of the FSM 1998 touring models, for the fuel injected bikes the stock coil is indeed single fire, it has three terminals on it.
one is power in at key on, battery voltage, the other 2 or trigger input for front and rear coil, the right side secondary terminal as the coil is mounted on the bike, is for the rear cylinder and the left terminal is for the front cylinder, make sure that your plug wires are in the right places, then check the 2 trigger wires for the ground signal that they get to fire the coil voltage to the secondary(spark plug), this isn't rocket science here. see my previous post.
m

 

 

 

This is the ignition system pick up/timer plate. I know that they call it the cam position sensor, but back before fuel injection, the name was different. How about a picture of your ignition coil?
m