Hmm - on the face of it, its easy to remove the headlining - just undo the sun visors, the mirror, the interior light and the sunroof surround and pull the trim plugs. They will pull out and can be reused but its far simpler to cut them and replace with new ones.
Unfortunately, to then get it out of the vehicle you really need to remove virtually all the interior trim as the centre roof trim section effectively blocks removal. To get that out, you need to remove the trim above the centre section doors and you'll also need to remove the trim around the rear windows to get the centre section clear.
To get the rear window trim out, you need to remove the rear seats and seat belt upper mountings! Reckon 4 or so hours work to remove and replace that lot!
(You MIGHT get away with just removing the seat belts and bending the trim back - you MIGHT be able to wiggle, bend and otherwise manoeuvre the centre section clear and then the front will come clear easily. You might also break and damage the window trim and centre section!!)
Before you do any of this, take a good look at the rear ventilation vents above the rear door if you have them fitted. Its worth pulling them out (take off the trim section above the rear door) and clean up the faces and then refit with new seals or use a decent silicon. They are a source of much water ingress when then runs along the channel which forms the top of the sides.
Also worth looking at the Alpine lights to see if they are leaking.
Sun roof leaks are often cured by removing the glass, give it and the rubber a good clean with soapy water and then lube the rubber with glycerine. Replace the glass, making sure its pushed well forward on its hinges and then leave it alone and do NOT open it again!
Other sources of leak are the joins where the various roof sections are joined.
Making a 90/110 waterproof is virtually impossible. Consider it a design feature to allow deep wading by letting the water out thro the various holes in the floor and live with it.
Have fun - Mike.