1. The body of Qui-Gon can not dissappear. As it has been mentioned, this would create more problems than it would fix. In addition, Yoda and Obi-wan pretty much evaporated soon as they were dead. If this is the norm, then he would have to dissappear in Obi-wan's arms in the reactor room. Otherwise, he'd still be alive when they put him on the pyre and would have died in the flames.
2. I've been trying to talk somebody into re-editing the Anakin destroying the Droid Control Ship for quite a while. Having Qui-gon speak to Anakin through the Force is the way the movie needed to end up. The allusion to Luke destroying the Death Star would be perfect. The only problem would be that in the final edit, Qui-Gon is still alive. He dies after Anakin destroys the ship. Having Qui-Gon 'communicate' with Anakin while he is still alive seems problematic. Moving the scenes around fix the problem. Incidentally, the revised 3rd draft has Qui-Gon dying before Anakin does his stuff.
3. As far as having Gui-gon communicate with Anakin or Obi-wan later in the movies....I think I'd leave the communication to a minimum. Qui-gon is a prequel character. If he is talking to everybody and appearing to everybody, then there's no reason for him not to be in the classic trilogy. If I had him appear, I'd have him only at the very end of the movie, As Obi-wan is walking back to the Eeopie. He'd appeas as Obi-wan walks towards him.