A long-shot guess.
Like windshield wipers, slide seals wear out. They get nicked at the crucial edge that makes contact with the roof, and they get stiff so contact is spotty. A nick could come from a small piece of debris left on the roof when the slide is retracted and before the slide "rolls over" during retraction. And, as many of us know all too well, stiffness comes with age.
If you haven't used a
slide seal dressing, it's possible that the slide seals are giving up the ghost.
You also mentioned that the rig is a "destination" trailer...which suggests that the slide is seldom, if ever, retracted, and this means that the slide seal is never "exercised" (flexed back and forth). It also means that the seal is ALWAYS exposed...never covered by the slide surround and protected from the sun. I know you ran the slide in and out during your repair effort, but if you don't retract it when you leave after your stay, the seal is sticking out there like a sore thumb getting baked by the sun.
You suggest the leak may be coming from on top of the roof. That matches the assumption that the seal may be failing from age, lack of exercise, and just drying out. Water can sneak under it because it no longer seals.
You've done a bunch of work on other parts of the roof system, and they, too, were sources of leaks. I don't know the age of your rig, but, given all that you've done already, I'd take a very close look at that seal.
If you suspect the seal is failing, perhaps you could perform a test before you replace it.
The tape for boat "shrink wraps" is amazing stuff. It's wide, so you could apply the tape to bridge the gap between the slide seal and the roof membrane, then test with a hose. If that stops or substantially reduces the remaining leak, the seal might be your problem.
Also...I agree with the suggestion to remove the gutter and renew the "caulk" behind the gutter and use better caulk in the screw holes. Perhaps also upsize the gutter screws from, say, #8 to #10 or #10 to #12,,,one size up from factory spec.
That's my hunch. For what it's worth.
PS. As KyDan suggests, definitely put a bubble level on the slide roof and check the roof pitch. The roof MUST pitch away from the main body of the rig, or water will dam up against the slide seal...making it all the more likely that water will find its way under the seal. If your slide roof pitches toward the main body of the camper, check your rig's level overall, and consider cheating the level to favor proper drainage. The roof on my slide has a pronounced pitch away from the main body of the camper. My slide actually appears to sag a bit, but that's how it's designed.
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