Help! I bit off more than I can chew! Body work

I would just put filler back in the seam on top of the quarter unless it has rust in it, then cut it out and put a new strip of metal in. It looks like it held up pretty good though. Someone put factory quarters on my 4dr dart many moons ago and seamed it in the same spot as yours, however they didn't do a good job (they overlapped the two panels) and it rusted so bad you could reach your arm into the trunk. Epoxy primer after you neutralize the rust would be the way to go, then you could do your body work over it. Anything out of a shaker can usually sucks.