I'm a little late to this but I'll chime in with a couple of thoughts:
Patberry, Looks like you did a great job on the roof and headliner and the insulation. I'm sure just getting the improved R value out of the rigid foam will pay in spades, not to mention the leak-proofing you did. You're blessed with space to work with, so you might feel fortunate when you are having to repair more than anticipated. Some of us, like me, don't even have the space to take the roof off or put our camper on saw horses. I live in Utah and really haven't challenged my camper with Northwest rains. I grew up in Portland so I know that if someone even cracks a smile, it might lead to a leak somewhere. So you can take some confidence as well knowing that your camper is battle-tested. If more leaks appear and you can identify the source, you might try Marine Rx. The marine repair industry has products for many of the same purposes we have, and they've done it for years for a well-moneyed but demanding market.
Regarding others considering replacing the headliner: I thought a lot about replacing the insulation and headliner for my Keystone but ultimately did not for various reasons. I was already working on so much else with the camper that it was not a priority. I did my re-wiring and new LED lights by making a few, small slits in the headliner and running completely new wire on new DC circuit and fishing it through. I just left the dead wire up there. I used clear patching material over the small slits, which did not work perfectly, but works. After good cleaning, it doesn't look bad, really. At least not to me.
If I end up smelling or detecting mold, then I will remove the headliner and replace it with new insulation. I'm not sure how I would do it, but I might consider doing it in 2 pieces (or more) with the seam running along one of the ceiling struts. The seam would then be covered by the wood trim. That might be a way to do it without removing the top. But if you could remove the top, I think the way Patberry did it is best.
