I've done this a bunch of times, and also had really confusing leaks. What happens is you have a leak in one place and because of wind, the angle of the truck, or perhaps black magic, the water will run down the aluminum and steel inside the upper parts of the box and then drop down somewhere else. Here's what I do, and it lasts for 5+ years.
Get a real nice carbide scraper, the ones with orange handles they sell at painting stores are good, also get one of the handles that has a bunch of interchangeable blades with different profiles. You'll also want a caulking gun, and atleast one tube of 3M 5200 marine caulk. get a small disposable plastic putty knife or two for smoothing out the caulk if you end up with an abundance.
3M 5200 is serious stuff. It's like a flexible epoxy caulk, it can be removed later but it's not the easiest thing. It can be used like glue, and it stays flexible for a very long times. It's also expensive. You also need to use the whole tube within a short period of time (short shelf life once opened).
I scrape as much of the old caulk out of the joint as I can. often it just peels out. I do the seals at the front corner caps, across top of the front curved piece, the joint between the corner caps and the long rail that goes down the top of the box (tricky) and then 4 feet down the top of the box on either side. If a leak persists later, I often will do another 4 feet down the top on the sides and see if that does it. Never had to go more than half way down a 24' box before I solved all the leaks.
Once you've removed the caulk to your satisfaction, ( it doesn't have to be perfect, just enough clear surface so the 5200 bonds well and so that the 5200 gets into the joint a little), apply the caulk. around the corner caps you'll probably want to apply an abundance to make sure you get a good seal and also sort of "ramp" it up to the edge of the corner caps, this will prevent puddles from being able to form right up against your joint. same in the channel on the sides where the rail meets the corner cap. Also, dab a bit on top of each rivet as sometimes a loose rivet can conduct water down into it and into the aluminum channel below.