Getting the top pulled up without tearing it is the biggest challange in this job. If you remove the window moulding and the vinyl top trim. Then you can get under an edge. With a heat gun and a razor blade/scraper, seperate the vinyl top from the roof, peeling it back far enuff to do your repairs. Sometimes it helps to split the top at the seam, (then reseal it with clear silicone when re installed). Tape off or cover the underside of the loose top material so no bondo/paint etc. gets on it. After you repair the sheet metal and everything is smooth. Re glue the top pieces/body (contact cement) and CAREFULLY heat and restretch the loose flaps back to their original places. Be careful not to leave an edge under the vinyl where the old glue and new glue meet. just go lightly or it will show. But too little and you will get an air bubble under the top.
Back when ,I used to do this quite a bit when doing quarter panel and/or rust replacement.