The primered one is backwards. The position those are clocked at on the wheelhousing determines the deck lid height when closed. Clocking them one direction or the other will raise or lower the deck lid so that it aligns with the rear window panel. also front to rear adjustment of the deck lid. You'll need to remove the torsion rods before you do any work on that. There's not a lot of material left to plug weld that. As far as I know they don't repop the lower piece. Franks might have one. Or I would section some new metal on that piece. There's a lot of tension on that bracket, needs to be strong.
Whenever I remove those from the wheelhousing, I always build a structure to hold them in alignment while the back of the car is apart. That way they can be welded back on the wheelhousing in the exact same position. I prefer to use steel but wood works also. I'm doing the Mustang right now. I used steel tubing tacked to body pieces that I won't be cutting out. Now when I cut the wheel housings out, I know exactly where Ford put them.
