I see what ur doing now, thought you could keep the scene where Qui gon meets Jar Jar - but if all thats gone now hmm...
So in case you cant roto him out... could you add the audio of him introducing him self to qui gon from that scene on naboo and put it somewhere while the're all on the queen's transport?
where he says "Mesaa your humble servant" - might come across like he's an assistant to the queen while on the starship...or something... not sure where you'd put it tho