Pulled it out of the chicken shed after 20 years. Took the carb off and used a complete can of cleaner and have it looking real good. Started on the third pull. But it has a hard time idling. Replaced the spark plug and changed the oil and oil filter. Have the air/fuel screw two full turns out. If I set the idle screw with it idling a little high, it will keep running. If I just turn the idle screw down 1/8 of a turn, it will idle down and eventually die. Any ideas on that? Also, when idling low it will seem to miss and make a hard clunk noise in the engine. Any suggestions? I have a video of it idling, but not sure I can upload.

Did you pull the jets out and clean them out real good? It could still be not getting enough fuel, causing the low idle. The clunk is probably the one-way starter clutch, it probably needs replacing but it's not a big deal, especially if you don't use the electric starter.

I just pulled the carb again and checked it all over and cleaned everything again. I also just check the timing and it is all lined up as it should be. Any other ideas?

Due to its age, the o-rings inside the carb are probably stiff, dry-rotted, and cracked, allowing internal air and / or fuel leaks. Replacing all the soft parts (o-rings, gaskets, and inlet & seat) will get everything sealed up again.

Bike Bandit or Yamaha Parts House are a couple of good sources for individual parts

I've been through this a few times with my old quad and bikes. I'm a connoisseur of fine old junk.