When I watched that video you sent, I noticed a couple of parts that are missing. I haven't gone back through all of the replies to make sure this hadn't been covered though. Without these being mounted on either side, not only does it open up a space for water, dust, exhaust fumes, etc., The innermost tab (circled) not being there opens this problem even more, because of the gaps just above the edge of the tailgate.
You can see in my second picture how close the tailgate sits on the edge of the lower window seal, it's not much. With the tailgate hanging a bit too low on that side makes the top edge of the tailgate/lower window seal even less.
With all of the water being on the right side, I'm wondering if it isn't the missing bracket/jamb is the culprit. But, with water flowing as it does, who knows. If it were me, and I wasn't able to make a trip to Florida to make a trade with a cool dude down there
, I'd track down those parts and order them. After the install, reasses. With the spare tire off.
Bear in mind, this is the '02 style hard top, so this would be how it looks on yours.
View attachment 128846
View attachment 128847