John, you are right on target. The water is accumulating in the trough on the inside part of the window frame. So, as I understand it, I should forget about finding seals, replace undamaged plexiglass bubble with a slightly thicker sheet of lexan, and then handle the sealing with caulking as outlined in your older post. Thank you for providing the link to your older post because when I searched this topic I did not find that post.
I'm also interested in hearing from other Dolphin owners too. I plan to assemble the responses and provide them to the repair facility to see which approach they are willing to undertake.