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Another random thought (I have lot's) ref the temp gas bottle you are using - is it "vented" - gas won't come out if air can't get in 

Is a pumper carb one with a accelerator pump on it? I DO have a accelerator pump on it and it seems to work fine when I bench tested it. I saw all 4 spit fuel out of them when I manually pumped them.

Random thoughts are good! It does have a vent on the cap. I also have a fuel filter inline with it and I can see fuel flowing freely. 

Might have just found your problem. On the VM26 with accelerator pump, they will not pump fuel till the #2 carb senses vacuum. You should not get fuel to the pump on a bench test. The sensor diaphragm might be bad. Item 23 here www.partzilla.com/catalog/kawasaki/motor...erator-pump-kz650-b3

I'm 85% sure the diaphragm is ok. I remember when cleaning the carb I looked at it and it was fine. BUT to confirm I'll look into it and report back.

Just thought of something. When I have them off should I LEAVE the 97.5 or replace it with the 102?

I’d stay with stock size Jets. It should run. Something else is going on. In betting air leak, lean condition. Post a picture of the plugs. When was the last time you installed new plugs. You can save fouled plugs by burning off carbon with a propane torch

wher is the temporary tank mounted. It must be above the carb fuel tee.

Ok I'm about to pull the carbs now. I'll attach pics of the plugs once I'm done with the carb. Also the fuel bottle is on the handle bars above the carbs.

Is the vacuum port on #2 carb capped. It normally goes to the tank petcock 

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It does not have a vacuum petcock.

Are you sure? I believe the kz650 with accelerator pumps came with a vacuum petcock. If you don't have a vacuum petcock, have you plugged the vacuum port on the #2 carb?  And if you're running from a temporary gas bottle, then you definitely need to plug the vacuum port.

On the #2 carb, there should be a port that feed to the engine side of the slide.  Don't block the bowl vent!  If you have this vacuum port and it's open, you will have a massive vacuum leak on cylinder #2.

EDIT: Photo stolen from this thread www.kzrider.com/forum/3-carburetor/60546...k-vacuum-line#757605

 

Ok have the carb off now. The accelerator pump diaphragm looks almost new. There was a little gunk in the square one but honestly nothing that I feel would raise alarms. 

The port is capped off on #2 and the 2 bowl vents are clear.

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This is a most bizarre situation you find yourself in, in my experience this severe lack of power would normally be "fuel starvation" - "massive over fuelling" or the timing a mile out but you seem to have bottomed out all of these 

Random suggestion #2 - put the old coils back on - if it returns to how it was then we are getting closer - if it doesn't then you have inadvertently created this issue and need to back track through everything you have done (man made faults are always the hardest to find  )