Atv ran well until it was left out in the rain. The quad has spark and is getting fuel but acts like the combustion is not large enough for it to start.
I have checked the timing and it is correctly set. Has new piston rings, head gasket, and coil. Carb was cleaned again and didn't change anything.
What could it be?

 

Check compression, with a rebuilt top end it should be fairly high but a mistake when putting it together could drop compression.

Rain can affect an engine in two ways, shorting ignition components so you get either no spark or a poor one and, if water gets into fuel tank through the breather, it will find the lowest point, the bottom of the float bowl, blocking the jets. When the "carb was cleaned again" did you check for water in the float bowl?