Starts 1st or 2nd kick but after warm up going through the gears, it just hits a bog all of a sudden, then I pull out the choke and it'll run fine? Carb and jets look clean?

There was a carb revision on either CT2 or 3 .
Can you list what carb jets are in your bike ( including needle and needle jet ) .
Also check the components are genuine Mikuni parts . they have a square within a square logo .

I would probably get a good rebuild kit and go through it.

A cheap thing to check would be the needle, seat and float - make sure the float level is really close to right. Also, that the needle and seat are clean and smooth, and that the float is good - no leaks or swelling.

Could you be starving for fuel - a clogged fuel filter?

Does still sound like the main jet is blocked or compromised at least. I hate to ask, but the main jet is in the side mounted--call it a bowl drain but not realy--jet is in that bung fitting. Make sure you remove it from the fitting & see if anything is behind it as the suck fuel from behind the jet--so back to front & stuff can sit behind & get drawn up to & block the jet, then drop away on a closed throttle. That's a bit of a guess & if you've been there done that then, i dunno. Raise the slide needle--drop the clip down.

That's exactly what happened when I first got my CT1 running a few months back. I had cleaned out the carburetor - I thought - but it had been so long since I've worked on one of these I forgot that the main jet was in that carburetor drain fitting.

It ran fine until I got up into 5th gear, then it would just bog down. I finally realized that the main jet was in the drain fitting, so I pulled it out, cleaned it up, put it back in and everything was fine. The main jet is in that drain fitting so it's easy to change, if you want to try a different size without removing the carburetor.

I'll throw out it sounds like the old carb bowl o ring might be missing. There is a piece which extends from the upper half of the carb into the lower, does this piece have an o ring on the tip of it, and is it in good shape? This o ring is critical, but it does allow us to swap the main jets w/o pulling the entire carb, which is a godsend.

Good point DARINM. Oring problems will make it go all rich. But i was stuck on it being lean & i could be quite wrong.