Is there any chance the problem is the coil?
I am not saying this is your problem (it probably isn't) but here is some info regarding your question about the coil.
I never had a HD dual fire coil in my hand to see how they are made, but if they are made like the schematic represents, you can have an issue with yours. The reason I say that is this. On dual fire, the spark plugs are in series with ONE secondary winding which has no center tap to ground. When you pull one spark plug wire, BOTH plugs should stop firing because one plug provides a ground path for each other. One plug is firing with positive polarity and the other plug fires with negative polarity.
If you pull a plug wire, you must connect that wire to frame ground in order for the remaining plug to fire. Now earlier you said when you pulled the front plug wire, the bike continued to run. And when you pulled the rear plug the bike died.
ASSUMING YOUR NOT DEALING WITH AIR LEAKS OR MIXTURE ISSUES,,, the bike should have died when you pulled either plug if the coil is actually made like the schematic represents.
If the secondary is completely isolated from frame ground and the primary windings, the above would hold true.
With coil still mounted to the bike, take a meter and check to see if ANY continuity exists between a spark plug tower terminal and FRAME ground & either primary wire stud. You should read infinity between either coil tower to frame ground and either primary terminal if my theory holds true.