Still a leaky ship...
 

Hmm..

I thought I'd taken care of everything you were supposed to with water ingress. I made sure the intake vent/cowl was covered properly (this was a leak - confirmed by a wet cabin filter - fixed that). I pulled off the A pillars - they had not been repaired so I took care of the last hole and then RTV'd the other fixing holes. The drain pipes for the sunroof look good - can confirm they have been replaced and that they are not blocked.

Yet still, after significant rain in the NW I have water in the lower channel (where the loom sits). Not a lot, but still enough. From what I understood, there is really only three places that water gets in - and I looked at these. There seems to be no leak from the rear drains either (and the back channel is not wet). The carpet is not soaked so the water has been contained to the channel.

The only thing I can think of is the sunroof drain possibly being cracked or disintegrating and letting in a drip-drip-drip. But I can't tell that unless I pull it - which I don't really want to do.

Any other thoughts?

I would take the time to attach a shield over the pollen filter box so that any water getting past the cowl (even if it looks fine) doesn't get into the cabin.

Blow out your ac condensation lines too. If they're backed up like mine were it'll leak under the carpet just like a sunroof drain backup would.

done and done. I even made sure by running some water off the cowl to make sure

have checked these. Not blocked. :).

Are your sunroof drains blocked at the top?

The sunroof drain lines can dry rot, allowing some water to seep into the car while still draining most water. Short of removing panels I’m not sure how you can rule this out.

Yes, this is my concern.

I know I checked the drivers side elbow and it was fine.

I will check again once I test the a pillar to make sure nothing was leaking in from there.

Does a leaking elbow wet the carpet or does it drip straight down to the wheel well?

If it's not fully rotted or detached it can do both. Fully detached will leak only into the floor boards.

It definitely will soak the carpet eventually.