Removing vinyl tops is a pain. On some car lines where vinyl roofs are standard, like 80's Caddys and your Chrysler, the roof panels are not fully finished, as a cost-saving measure, since they will be covered up anyways. So, even if you remove all the padding and glue, the roof panels may have rough, unfinished seams.
Try going to a good auto trim and interior shop. They can install another vinyl roof quite easily.