I painted my texture and then wanted to use the Ambient Occulsion Bake option to add the lighting effects but after the bake the whole model was the gray colour. How to I maintain my paint job?

I recommend keeping your paint job as its own texture and bake your ambient occlusion as a separate texture. It sounds like you're trying to bake AO into the paint job texture so they're combined in one texture.

I'm not aware of a straight forward way to bake the two maps together. There's several ways to combine separate textures with photo-editors like Photoshop, GIMP, and Krita. You could also do it with Blender's compositing nodes, but that's arguably the harder way to go about it.