We had a steady rain overnight, but it dried out a good bit by this afternoon so these pictures aren't that great at highlighting the amount of water that has gotten inside the bed.
1) Picture 1: This is the primary entry point for the water. The cover does not sit flush with the driver-side of the tailgate. This part of the cover is elevated by maybe a centimeter or two compared to the passenger-side. Look at pictures 3 and 4 for comparison of the driver and passenger sides of the tailgate.
2) Picture 2: Where the truck cover folds, there is a slow drip where my finger is pointing. Nothing looks out of sorts at this area of the truck cover, but water is dripping in due to some sort of weakness.
3) Picture 3: While it may be hard to tell, the driver-side portion of the cover and the tailgate have some spacing. I took the tonneau cover rail off and put it back on and it looks like it is installed correctly, but the driver-side of the cover is elevated by a few centimeters over the tailgate. I did eyeball the tailgate, and the driver-side actually looks slightly lower than the multi-pro part of the tailgate when compared to the passenger-side. If that is truly the case, then it may not be a cover issue but more of a tailgate issue.
4) Picture 4: While you may not be able to tell, the tonneau cover and the tailgate are more flush on the passenger-side and water is not getting inside the bed.
When they took the first cover off and pulled out the rivets, the rail cap does have an elevated area at the site of the hole. While the tonneau rails do not appear to be uneven as a result, I can't help but think the auto shop's screw-up is impacting this new cover. This is probably no help to any of y'all at the moment, so I may take the darn thing off again and take pictures of the rails without the cover and its related parts.
Thanks for you taking the time to look at this. If anything, it's an opportunity for me to blow some steam off!