Back window rusted and leaking???

Ok so there's after I pulled the old ugly sundried vinyl top off, I found a few holes around the back glass on my swinger and I'm a little confused on what to do here. The window leaks through the holes obviously but also around the bottom left corner of the window. I want to take out the glass, patch everything up nice, get a new seal, trim clips and then throw a vinyl top on but i'm not sure how to go about it or if I even should. At this point the trim is out but the clips are mostly bent or broken.