I had the same thing on my Challenger. To repair it properly the skin needs to come off. You will probably be shocked at the extent of the rust. Also unless AMD or Dynacorn has recently reproduced the inner structure, start looking now. The parts are tough to find. Once the skin is off and you have the replacement parts the actual repair is pretty straight forward. A lot of spot welds. My roof skin looked pretty good by the way but the inner structure was gone. Before I removed all the weather stripping channel, I could not see any rust. It was all hidden just like yours.
Wes