Hi gmblu - Did you get your no spark condition sorted? 2+ weeks is too long to go with a bike down this time of year! If not, have you checked whether or not you have a signal going to the IC igniter box from the ignition pickup at the end of the crankshaft? To get spark at the plugs, the first three things you must have are a spinning crankshaft, a working ignition pickup, and a good wire going from the pickup to the IC igniter. If not, you wont ever get spark at the plugs. When the crankshaft spins, it has to have some way of telling the IC igniter to trigger the coils to release their pent-up pixies and send them to the spark plug(s). To get the "FIRE!" signal from the crank to the IC igniter, your KZ1000 uses a magnetic Hall effect sensor system. That is, as the crank spins around, a magnet on it or in the sensor (or "pickup") bolted nearby induces an electrical charge in the sensor. This charge (or signal) goes by wire to the IC igniter and tells (signals) it when to discharge the coils into the plugs. So, some things to check: 1) sometimes the Hall effect pickup goes bad, in which case no signal is getting to the IC igniter, which means no spark no how.; 2) sometimes, though rarely, the gap between the crank and the Hall effect pickup gets too wide, usually because a screw got loose, and if the gap is too wide for the magnetic field to be established, the Hall effect sensor never senses that the crank is spinning and thus no "FIRE!" signal goes to the igniter.; 3) sometimes the wire between the Hall effect sensor gets melted, abraded, or otherwise damaged and can't get the necessary signal to the igniter.; and 4) sometimes the crank seal located behind the ignition pickup parts goes bad and leaks oil into the ignition pickup area, basically flooding it and interfering with the magnetic field.
If you need help figuring out how to test for signal getting to the IC igniter, or measuring the gap between the crank and Hall effect pickup, I'd look in the shop manual, or post again and I'll see if I can dig up that info. I thought there was a KZ1000 shop manual posted here, but I don't see it.
Also, and though I'm not entirely sure about this, I don't think I would run the extra ground wire as you described. I'm not sure, but you might be cutting the coil out of the circuit entirely by accident. Not sure. You're spot on to be concerned about a bad ground, though. What I'd do to ensure a good ground path in this instance is run two jumper wires (alligator clips on lengths of plain old 14 gauge wire would work fine here) as follows: one between the ground wire for the coil (with the stock ground wire still attached to its coil) and the negative terminal of the battery, and the other jumper from the negative terminal to the cylinder head.
I hope this helps.