I have water leaking in at the seam where the two halves of the top come together and meets the drivers side window. The passenger side is fine. It's also whistling at the top where the rear-side and driver side widows meet. I am guessing that both issues have to do with the top being out of alignment. The Haynes manual talks about aligning the top, but the information is sketchy. Is there a Chrysler manual available that shows how to do this?

 

Probably more likely due to your weatherstripping getting old and hard. Could also be window alignment. These topics are covered in the Chrysler manual but it, too is somewhat "sketchy". For example, to align the windows using the procedure recommended by Chrysler you must remove the weatherstrip. The manual simply says remove the weatherstrip but never tells you how to do it. You might have luck finding a shop manual on eBay as they come and go occasionally. The Chrysler shop manual is divided into several volumes, and the convertible, to the extent it is different, is covered in its own volume. Shop carefully for a manual.