Finaly got to test run the CT3 and it was pretty good. I noticed about 1/4 throttle it kind of sputtered. I pulled the plug and it was running rich. I have @ 30:1 ratio for fuel.With idle at about 1600 I adjusted the air mixture screw ( original was 1 turn out ) and it took about 3 turns out to raise the RPM's . I pulled the carb and and raised the jet needle setting to 3 ( original it was 4 ) and the air mixture setting went to 2-1/2 turns out. It is a lot more responsive at 1/4 throttle. These are the jets that are stock in this carb. Main Jet: 4/042-210 Pilot Jet: VM22/210-40 > I was hoping to not have to play with the jets. Is 2-1/2 turns out on the air mixture a bit much? Should I raise the needle adjustment 1 more slot? I can't take it for a good test ride so I was going to go with a new plug and run it around the block to see if it is still rich.

Umm...  yeah you really should read the tuning manual.  Circuits overlap but somewhat independent...  not good to try to adjust the idle to 1/4 mixture with the needle.

First step is go to a smaller pilot jet.  From what you're saying I'd guess a 30 would be good.  What does your original carb have?  Try that one.  Air screw should be close to 1.5 turns out. 

I don't have the original carb. It was trashed so i purchased a VM24-512 . The bike lived at higher elevation than where it is now, so just trying to find the sweet spot from anew. So I can grab a 30 and give it a shot. I thought Mikuni would start at a neutral point with the needle adjustment. I was surprised to see it on the rich side. I also expected to see the air at 1-1/2 turns and it was only 1. Good advice thank you.

A "trashed" carb still might have jets in it. 

Unless you actually threw it away. 

Standard jetting on the CT3 is main jet 230, pilot 25 and air screw 2 turns out.
Needle clip position 3.
I appreciate your Mikuni isn't the stock Yamaha one.
It's worth having a look on the Mikuni website and reading the info they have about how the different jets and needle positions interact and how they affect operation at different throttle positions, it may save you a lot of time getting your bike running well.

I actually recycled the carb to another user for parts. I ordered the 30 pilot . I am going to to keep the needle adjustment at 3 and adjust the mixture as neeeded for max rpm's and adjust the idle to 1600. From there I should be close as the bike ran very well but the middle just wasn't there with the rich mixture. Thank you 

You might ultimately end up with a 25 but a 30 would be my guess from what you've said.  Do you know the slide cutaway?  2.5?  3.0? 

Hopefully the rest of the jetting will be close then too...  might still have to drop the needle a slot but fingers crossed it will run well.

They come rich because many people try to put a bigger carb on a smaller engine that isn't designed for it.  The vacuum signal is weak which requires rich jetting. 

Mark once again you redirect my thinking to the right direction. I am not sure of the cutaway but if I am on the right track I should remove the idle screw and measure the cutaway gap. A 5/32 drill bit should equal a 2.5 & a 3/16 drill bit should be a 3.0. If this is correct then that should help direct the initial air flow before adjustment. Am I going in the right direction?

Or just look at the number stamped underneath the slide... 

I was just asking to compare to stock CT3 carb... it looks like VM24 512 specs say 1.5 which is a pretty rich slide.  That affects the transition up to about 1/4 throttle the most. 

On the main, it's impossible to compare to stock because the needle and needle jet are completely different.