Perhaps Qui Gon has only recently learned how to make contact from beyond, maybe it will be all related to Anakin's statement after his mother was killed. "Someday I'll even prevent people from dying." (not quoted exactly). Maybe the chosen one keeps everyone he cares about hanging around. Qui Gon did free Anakin.
Clearly pretty much everything, to judge by the final scene of the two of them together.
That was a three line scene. It basically told the audience nothing except that the two of them are in cahoots. It in no way hinted at how much Sidious had confided in Dooku. He may have kept him up to speed up until the war started (I dont think so, but maybe), but I think Sidious set Dooku up for a fall from the beginning.
GL sayd in the making of EPII that yoda hears QGJ voice to create a link between Anikins evil side (This boy is dangerous) and QGJ's stubornous to teach the boy after the council told him NO.
By the way not only did QGJ not dissapear but none of the jedi's killed in the arena dissapeared when they were killed in EPII.