TOPIC:

Ray,
Get an inline spark tester.
Testing spark outside of the cylinder isn't reliable. This other method is a little better as the plugs are actually seated in the engine.
You may have to rig metal end of the tester as the tip of the tester does not have a removable terminal nut.

What is the story on your plugs and wires?
Which plugs did you get?
Which wires did you get?
Which spark plug cap did you get?
Are all of the above items new?

Put you meter on ohms.
If possible disconnect the spark plug wires from the coils( do this if you know they can be disconnected-some wires are not meant to be removed from the coils)

Put a probe on each end of the spark plug wire with the cap on and measure the resistance. Just checking your secondary side.

Just thought of something.
I need to check how good of a ground your cylinder head is.

Key on /ignition on
Meter DC V
Black probe battery negative post
Red probe positive battery post
Note voltage

Move black probe to cylinder head near spark plug hole.
Note voltage
These two voltages should be very close
If not, then you do not have a good ground connection to the cylinder head. This wouldn't make much sense as the engine case has a good ground. But earth is a weird place so we'll check it anyway.

 

I would suggest putting it all back together, clean the carbs, install the tank and see if it fires. You might find the coils are switched but should get a pop out of it. Switch the HT wires and try it again. It's easy to micromanage things to the point of chasing your tail and getting nowhere fast. 
BTW for years I looked for the cause of a miss at mid throttle. I used a timing light and noted the lack of flash corresponding with the miss. Turned out the spark advance springs were weak so I corrected them and low idle was better. At 3/4000 RPM the miss was still there. I did the coil/relay mod and the spark is stronger but the miss was still there. Back in the 90's Miller said it sounded like it was electrical so I kept looking at connectors etc. but I couldn't solve the miss issue. It wasn't bad enough to feel it just annoying. After getting my 33's dialed in and all the crap that involved the bike ran better than ever still the miss persisted. Tried switching air jets {these carbs they're replaceable) a member has some for the other VM carbs and he also repairs the starter plungers (choke plungers) being they can leak causing the same issue. I ordered new ones from jetsrus.com/ and the miss is all but gone. One step up on the air jets should cure it once and for all. 
My point is it's easy to chase ghosts and miss the problem that;s why I'm suggesting to get it running then solve the issues as they present themselves. 
Good luck and I want to hear it run. 
Steve
 jetsrus.com/individual_parts/002-670_su.html

Good morning gents,
Thanks to all for the comments. I appreciate all the feedback and will work on this today and post some measurable results, heating up the garage now. Yesterday got away from me plus it was 15 degrees so the garage was fridged, Pouring rain here , a bit warmer and my NFL team is not making the playoffs so no important games to watch today, for me anyway! I am going to work on this for most the day, I hope I get some spark. Let me see if I can track down the clicking noise. I am going to take new readings and post.
 

@F64, @Mikaw, @Wookie58, posting more results shortly.

Good morning @F64,
below response to your questions
What is the story on your plugs and wires? Plugs came with the bike and look new, NGK B8ES
Which plugs did you get? NGK B8ES
Which wires did you get? Wires came with the new coils from 4into1.com/4-ohm-coils-and-caps-kawasaki...-gs550-750-850-1000/
Which spark plug cap did you get?  4into1.com/4-ohm-coils-and-caps-kawasaki...-gs550-750-850-1000/
Are all of the above items new? yes all new

Put you meter on ohms.
If possible disconnect the spark plug wires from the coils( do this if you know they can be disconnected-some wires are not meant to be removed from the coils),

It doesn't appear these can be removed.

Put a probe on each end of the spark plug wire with the cap on and measure the resistance. Just checking your secondary side.

Just thought of something.
I need to check how good of a ground your cylinder head is.

Key on /ignition on
Meter DC V
Black probe battery negative post
Red probe positive battery post
Note voltage 12.01

Move black probe to cylinder head near spark plug hole.
Note voltage 11.99
These two voltages should be very close
If not, then you do not have a good ground connection to the cylinder head. This wouldn't make much sense as the engine case has a good ground. But earth is a weird place so we'll check it anyway.

Cylinder head has a good ground.

I'll have you check the points next.
I'm not sure the points are supplying a good ground to your coils.

I'll have to show you where to meter from. That'll be maybe an hour from now as I have to mark up a screenshot.

Meter on ohms
Key off ignition off
Pull the spark plugs out of the coils.
With the left coil.
Put one probe in the spark plug boot touching the clip.
Put the other probe in the other spark plug boot for that coil.
What is your resistance in ohms?

Do the same for the right coil.

Just checking the secondaries of the coils.
Making sure there are no breaks along the wires and a good connection to the boots.

I'll work on getting the screenshot to you.

Measure the gap on your points with feeler gauges at their widest opening.

@F64, gaps are set at .028 which is within recommendations.

Thanks

Key on/ignition on
Meter DC V
Points closed
One probe on red circle(put probe on the wire terminal)
Other probe on the other red circle part of the plate.
Note voltage

Open the points
Note voltage

Do the same for the other set of points with the green circles.
Points closed
 Points open

Turn off ignition
Wait 5 min to let the coils cool off. Probably less time considering how cold it is there.

Turn ignition back on

Points closed
Put one probe on the wire terminal in the red circle.
Put the other probe on the negative coil terminal for that set of points. The wire color attached to those points should match the negative terminal coil wire. It's either green or black.
Note voltage


Do the same for the green circle wire terminal and the other coil negative terminal.
Note voltage.

Turn off bike

The first voltage drop test is checking the connection from the wire terminal through the points contacts. Closed, the reading should be very close to 0.0v
When you open the points you should see battery voltage-12v

The second test is testing the wire from the points to the coil.
Closed points, close to 0.0v

Image courtesy of Z1 enterprises
 www.z1enterprises.com/points-breaker-ass...y-z1-kz900-1000.html

Thanks @F64
readings to follow.