Hello All. I am attempting to bring an AT3 back to life. I have rebuilt one carb, and then outright replaced it over this issue. The bike will turn over and run with choke pulled but the idle runs up uncontrollably and the ignition has to be turned off so it won't redline. If you put the choke back in it dies. I am new to wrenching beyond just replacing parts, so diagnosing this is out of my league. Any help would be appreciated.

Welcome, there seems to be a bit of that going on lately. Must be the time of year. Sorry i'll stop being stupid. There's not many things to cause that. First is the idle speed screw turned in way too far--that's speed not mixture screw. Check the throttle slide it hitting the bottom or look through with carb in your hand & shouldn't see light under the slide if right down. I doubt its an air leak anywhere close to the carb as would need to be a big one plus it needs fuel. Crank seal could have been pushed out behind the mag on the left or partially out at an angle & letting air in. Right out & it wouldn't run at all. Same with right side crank seal but would smoke in a big way. Need a bit more info or a video. I'm probably forgetting other possibilities like base gasket broken or popped out at the cylinder base but you'd see that hanging out or sucked in likely along the side rather than front or back. Out of ideas for now.
Re-reading your post i'm leaning more to a crank seal fault. They don't wear out enough to go like that in my experience but if they pop right out or partially then likely is the problem.

Air leak.  Probably crank seal. 

wish i could wright short stories lol.