Here is another issue that resulted from the new roof. I had new roof put in around october 2018 and didn't drive much due to winter, so just put the car in garage. After taking it out in the spring of 2019 (May) I noticed a squeaking noise coming from the passenger side window area. It only seems to happen when it rains and the roof gets wet. Once I hit summer, it’s been pretty dry so I almost forgot about this issue. Now that it's fall and it rains this issue is back. When I got the new bungees installed I asked the technician to look into squeaking but he said he didn’t hear anything (it was a raining that day). See video below.
https://youtu.be/aUICTXZa0A0