Leaky Canopy

The canopy ion my truck has started to leak and I am suspecting that it is from the tracks for my kayak rack. I noticed several small areas of water after big storms this winter. I am wondering if there are any suggestions of how to re-seal the tracks? I am looking at using silicone caulk between the track and the canopy or just spraying the whole track with flex seal or other rubber sealant. Wondering if anyone has any advice or recommendations of techniques or products to use. The reason it is of concern is that I use the truck canopy as a camper and would like to keep gear dry.  Or I could just go camping when it isn't raining!!  Thanks in advance!!

My canopy started leaking some time ago.  I thought it was the yakima clips I had installed.  Turns out it is the windows that are leaking.  The canopy is 17 years old, fiberglass, and has taken a lot of rattling and abuse so I'm not surprised.  I used silicon to seal up the clips but have not yet tackled sealing the windows.

With the nice weather I pulled the tracks off the canopy, cleaned it up, and slathered the bolt holes and underside of the track with clear silicone. It is a two person job to re-install the tracks, one inside and one outside. I decided to not use the flex seal because it didnt have an UV protectant. Now wait for the caulk to cure and hope for a rainy day to see if my effort paid off!!