FWIW, I recalibrated the sunroof at least a dozen times when I had the same issue with my 2005.. I was positive it was the sunroof leaking, until I dropped the headliner so I could see EXACTLY where the water was coming in from when I ran the hose across the roof.
I was surprised to discover it was the seam where the A-Pillar meets the roof (right at the upper corners of the windshield), not enough seam sealer was applied from the factory. The sunroof (at least on mine) had never been the problem.
10 minutes with 'flowable' silicone windshield sealer and my issue went away completely.
Of course, YMMV.
2005 WK Limited, 5.7, QDII , 2" BB, 255/70R18's on JK Alloys <<== SOLD
Silver WK Club Member #116