plugs 3 & 4 not producing spark

Damn, it's NOT the igniter. i just pulled it from my broken KZ1300 to my working KZ1300 and the igniter works fine. Great spark on all 6 cylinders.  ugg...   

Ideas?

I removed the blue & pink connections and instead put the black & pink connectors (for plugs 1 an 6) on the coil for plugs 3&4. Low. and behold, I got spark

Did you try the other way around? Put 3&4 on 1&6 and see if there is spark? I mean switch them and see if anything changes.

Yes, I tried that. Plugs 1&6 show no spark while 3&4 show spark with it switched.

You have a 5 pin connector on the ic ignitor and the blue lead to 3&4 is the no runner so I would pull out the ohm meter and check the resistance on the leads coming from the 5 pin connetor to the 3 coils. The resistance should be next to nothing.  There's a bad connection or a broken wire. Something like that.

Thanks Kawboy, I'll give that a try here in a little while.

Bear with me - there is a 'Point" coming regarding your Ignition problem.
I just finished a pains-taking and somewhat aggravating collective 20+ hours trying to find the bastard connection (or what ever) that has been plaguing me regarding that dim (Damned) left turn signal indicator ( in the Cluster). Mentioned this recently. Every time I thought I had it fixed - NOPE - Always worked for the first 15 -20 minutes after I had done "something" and then started acting up again. Sometimes so bad the rear left indicator wouldn't flash, either. Isolated to the left side only. Confusing the issue: unplug the headlight and the signal was like strobe AND the Four-ways.....No problem! Every connection, terminal, ground etc meticulously cleaned and inspected. Using "jumper-leads" to by-pass some of the harness connections I could get the indicator and signal to flash bright. Basically had everything apart from the instrument cluster to the tail light. AND REPEAT - because it's easy to miss something when the panties are around your neck and your ready to scream !
Hours studying the schematic !!!! Then the F*^%Kn' light-bulb went on ! (Pun intended) The one damned plug I had used for the jumping and metering (9-terminal / 8 wires) was giving me weird and inconsistent readings for V. & R. Turns out, ONE wire terminal had come unlocked from the plug body - not allowing a full connection. Couldn't see it until I unraveled the group and straightener out all the wires. The headlight was putting enough load on the harness voltage that the lousy high resistance connection got robbed of Voltage and Current !
SO......I think you've got this figured out by now: If the ballast-resistor , Ignition-triggers, and Igniter are good....then check each plug terminal that the dead cylinders are connected to and look for a terminal that's pushed out of the terminal block or a bullet-plug that's too loose or maybe even has only the insulation holding it together.
Really hope this helps.

AND....WORKING THIS MORNING BUT NOT NOW - I'm referring to ATTACHMENTS and TOOL-BAR !!!!!