Setup is correct.
You're putting NEW, bigger bundy tube through? If so remove the old small one, use it as a template to bend the new stuff, then put it back in were it was. Clips should still be fine for the bigger tube.
Yes use rubber hose to connect things up, just use the bundy tube for the runs under the car.
If I were to simply run the rubber tubing through the cabin, would I be able to get it through engineering?- Most deffinately not..... even in Tassie.