plugs 3 & 4 not producing spark

Thanks everyone,

So I think the problem is in the pickup coils. I traced the green / light green wire to the ignition coil for 3 & 4 (according to the manual).  I went back and checked the settings and the green / light green wires show zero on the multimeter. The other 2 pickup coils are in spec with the manual ohm setting.

So now comes the next question, how do I get pickup coils (also called pulser / pulsing coils) ?? Anybody know where to get a set? 

I think Scotch has mentioned before that the pick up coils are common to other models, such as the KZ1000. If you search the forum, you’ll find the information.

Well, here we go.

you posted checking the pulser coils and found 
Green -> Light Green = 451
Red -> Yellow = 423
Blue-> Black = 419
Now you found an open circuit. That's indicative of a broken wire. When you checked it the first time, it tested good. Second time bad. Put the ohm meter back in the leads and wiggle the leads around (bending twisting the wire) and watch the ohm meter. When you see the meter go to open circuit, you've found the break. So then go fix the break. Better than spending time locating a coil. I'm all about "fix what you can, replace what you can't"

I got a replacement ignition pulse coil trigger from a bike salvage yard but that was WAY back. You might get lucky and find an era correct Kawasaki buried in the weeds at a similar bike recycler.
If the "broken" wire is internal to the trigger winding's, as I suspect it is - It's "Toast".

I guess it's been already sorted or suggested, but I'll just shoot again.
From what I understand the pick up is good after testing on another bike, the coils are good.
Did you also switch just the red wire between 3/4 and 1/6 on the resistor. If then the 6 has no spark but 3 has, then it points to either that one part of resistor broke, or that red wire broke (if the colored wires had been sorted out).
I'm not an expert, but superficially to me it points to something with a wire itself, or a wire connection. (if that part of coil connected to coil with a red wire is good)
Real life example.. Just a couple weeks ago I had pretty much the same scenario on my Vmax. Except that one cylinder was quitting randomly when riding. I had COP's installed, so the power supply was sitting directly on the coil. Just touching it would solve the problem temporarily. After an x number of kilometers, problem would return. All indicated a loose connection going bad due to vibrations. I removed the wires from the electrical connector (also two - coincidentally red and colored as well), and the reason was obvious. The crimp had one of the 'ears' broken off, and the naked wire end was moving freely inside the crimp, eventually came totally out. In my case, I soldered it and problem fixed. 
So, I would check every connection and connector, the wire itself for internal break, and that part of the resistor. It could be something simple.

Ok, after re-reading some of my own posts (thanks Kawboy!) it would seem likely that it is a bad wire (likely light green one) between the igniter and the pickup coils.  Anyway I got a busy weekend ahead but I'll get to it and let everyone know if I can find it. 

Thanks again for all the help!