Just a quick note. For shaping up the door, and perhaps the quarter too, you could buy a profile gauge. The longer the gauge you get, the better. It lets you copy the profile of a good panel, so you can use that as a guide to shaping up a damaged panel. And you could copy a profile on a piece of cardboard and use that, and make other copies of different locations. So, you could copy the profiles of your driver side to compare to the work on the passenger side.
And for the rust hole, best would be to cut it out beyond the rust, cut out a metal patch to fit the hole, like a puzzle piece, and weld it in.