Sputters at 0 to 1/8 throttle. Runs great from there up

We are also assuming all valve clearance's in spec assuring good compression on all cylinders with new plug wires, etc. (unless other wise stated)

The Color Tune is a spark plug you can "see thru" the top of it, you can adjust the fuel mixture to be the same "color" (optimal burn) on all the cylinders.

Ordered a color tune yesterday, going to go from there. Thanks for all the advice, I’ll keep everyone apprized at how this turns out.

Okay, I first want to thank everyone for all the help. I ordered the color tune but it is taking forever to get here from U.K.. Hopefully I can be a little better at describing this situation. While I am waiting I figured I would try to go over everything I could think of to do. I took the carbs apart again cleaned thoroughly and changed the jets back to what was in there to begin with, which were 113 mains, 15 pilot and needle in 4th position. I then checked the valve clearances and all were in spec other than 2 & 3 intake which I couldn’t even get my smallest feeler in which is .038 mm. Book says acceptable is .05-.10. Thus, I ordered the little tools from Z1 to get those shims out. #2 is marked 255A and #3 is 250A, not sure what that refers to as when I measured the one marked 250A it was 1.4mm. My question is what do these numbers refer to, and how do I determine which shims I need to order. 

Shim thickness is measured in mm. 
2.55 mm thick and 2.50 mm thick.

​​​​​​0.05 minimum gap was changed to 0.10 minimum in a service bulletin. Gaps should be between 0.10 to 0.15. Err to the larger size. 

Either you mismeasured your shim thickness or somone has had the grinder out which is a definate no no. 

To increase the valve gap you need a thinner shim. To decrease the valve gap you need thicker shims. 
Shims come in thickness size steps of 0.05mm.
Eg. 2.50 - 2.55 - 2.60 - 2.65. 
The thinnest shim I've seen is 2.30 and the thickest is 3.20.

Yes, you are correct, I mismeasured. So, that would mean all my  valves are too tight?

If they are below 0.10 mm, yes they are too tight. 

I have a 1978 kz1000a with pods and 4 into 1. Mine bogged too. this is what got rid of the bogg.

1-15, 122.5, clip 2
2-12.5, 122.5, clip 1 (richest clip)
3-15, 122.5, clip 1 
4-12.5, 122.5, clip 2

i think what im calling clip 1 is technically clip 5. 1 should be leanest and 5 richest. I numbered in reverse. 

A warning, make sure the carbs are sealed, caps are on the top, pods on, and synch ports have a plug. I couldn’t tune anything to the right afr with those things off. 

if you want to see fancy graphics that describe the bogging down on cylinder 2 and 3 go check out my build in projects.