Hi Fat Tire,
Sorry to hear about your troubles.
I am not sure how many here will have had experience with the bunk end seals on that trailer as it is a Dutchman aerolite. Yours may or may not have seals similar to a Forest River Roo, Shamrock, or Surveyor model hybrid. I'm sure the doors are a bit different, too.
The first thing you need to do is isolate the cause. In general, first determine that the water is an outside leak or if its condensation.
Assuming this is not condensation, determine where it is coming from.
You say the top. Is it the throughout the top? Is it the middle - possibly indicating the bunk door is bowing so that the middle is not making a tight seal.
Are there any soft spots? Are all the screws caulked well? Is there a gutter above the door when closed and is it damaged?
This could also be a leak in the the roof or outside lights that is showing up at the top.
I wish you the best of luck. Leaks are no fun and its good you are tying to figure this out before too much damage.
DW, 3 Kids and our Goldens
2012 Shamrock 233S
2008 Toyota Sequoia 5.7L 4WD