in your picture with the tarp it looks like the passenger side wiper cowl is able to allow water into the cowl area. right under that part of the cowl there is a access panel that covers the A/C air box inlet /blower motor. sometimes that cover gets detached and allows water to come in through to the inside of the truck.
was it the front passenger foot well side that was wet?

 

I would check your rail bolts since you didn't have the back covered

 

If I were you, I would sit inside the truck next time it's raining, now that you have the interior torn apart, and just watch to see where the leak is coming from. That is how I figured out the leak in mine, it was coming from my top window rubber seal. I had a hose running on top and I sat inside and waited for it to leak. I siliconed the door seal and it has never leaked since

 

2005 Hummer H2 with Sunroof
152k miles
Recently ran into an issue with water leaking in from the roof. True source was unclear as weep holes were clogged on both side and running light gaskets thickness appeared to be insufficient to seal with the roof.
Tested both of these for an hour running hose and sprayer to the top of the truck; no leak after doing these!

Solution for weep whole cleaning quickly:
- Find some old Coax TV cable and cut 6 to 7 feet from it. (example picture below)
- Used used CATV 18 AWG cable and left the coax connector on the end to make easier to grip
- The cable fit into the weep holes perfectly. (got the idea from a Sonic Straw that fit into the hole and was the same diameter as the coax cable)
- Was able to run it all the way through and clean out the weep holes in about 5 minutes

Solution for water leaking in through running lights:
- Ordered another set of gaskets for the running lights (full set for all 10 running lights)
- Link for gaskets used: - Doubled up the gaskets by carefully aligning the new ones to adhere to the bottom of the existing ones.
- Note: The existing running lights & gaskets were about 3 years old. Had replaced them.
- Re-installed the lights
- Did have to carve out 1-2 mm on some lights on the non-sprint loaded side to get them to lock into place

Hope this helps someone who may run into the all to common water leaking in problem.

 

I have been here. Biggest culprits for my 2008s leaks were the clearance and market lights. I replaced all of the gaskets with ones recommended by members here that are extra thick, found on amazon.

next I silicone sealed all of the clearance lights to the roof with a clean bead around each.

Also and this has been huge. I purchased DampRid closet hanging bags and keep them inside the cab to absorb moisture and prevent mold and mildew from forming because of the moisture. I refuse to grow shrooms in my carpet.

another member here advised that he used flex seal tape to seal off the corner marker lights where the original wiring plug had deteriorated. Definitely sounds like the best fix yet. If my silicone seals fail on those corner, I’m going to use his process.

Hope you find the source, aside from the lights it could be the rain gutter seam tape. If it’s cracked and you have dark spots on your headliner it’s likely the seams need resealing.