I'd ditch and edit out all references to Obi-Wan not already being a Jedi Knight.

They could just be two Jedi paired up for the mission (one a bit more reckless and less experienced).

It would keep Obi-Wan as trained by Yoda exclusively and knock away many layers of EU nonsense to justify Qui-Gon as his Master instead.

In an ideal world he would have found Anakin and Qui-Gon would have remained on the ship and been the voice of caution but there is no way to do that without remaking the film from scratch.

Having the student kill the Sith Lord that bested his Master makes very little sense without many years between the two events.

I'd also make the blockade more personal (perhaps not the whole Trade Federation were behind it but they later get tarred with same brush, when the Delegate claims ignorance to the Senate he could be telling the truth) so instead you could put the blame on Nute Gunray, the greedy Viceroy Of Neimoidia.