As the rear worked for a while I would check all the wires, connections and grounds first. Look for corrosion and dirt build up, the connectors on these bikes are really cheap (no silver or gold plating on the contact) and definitely not waterproof so they get a layer of corrosion very easily.
If you have a decent meter you should be able to see the pulses from the ignition module going to the coils.
You mention rear coils produces spark in front, did front produce spark in rear?
'99 Vulcan "Victoria"