@United232 as many others have said, thanks for the in depth info.
I recently went overseas for three weeks to find that, following some intense rain before we left, the interior of our yeti had turned into a petri dish, sprouting a forest of mold throughout the interior. And it's almost certainly due to water that was pooling in the foot wells unbeknown to me. Not nearly the amount of water as in your case, but enough to spread beneath the carpet reaching as far back as the rear foot wells.
And so now I'm embarking on the remediation of our sun roof and stumbled across this handy guide!
I have identified that the drain hose on the nearside front is indeed blocked, so I will have to sort that out, but I also plan to make the repairs outlined in your report (which I've read with much interest) as i'd rather not take the chance of not sealing these gaps while i'm at it.
I have begun the process of removing the headlining to check the seals on the drain tubes and trace them down to free up the blockage. However I have hit a snag with the sun visor arm bracket removal. I've taken the screw out but the arm clip that recesses into the ceiling is stubborn to the point that I'm afraid i'll break it if I pull any harder, despite wiggling it every which way. Any tips? I've read about others on this forum who've had the same problem...