Installing replacement 1/4s?

Hey Sin, that 'joggle' will work. On the tops of the quarter make real sure your panel is in the right place. Get a spot welder and hit the seam making sure the panel is as tight as you can. leave a couple of inches between the spot welds and skip around some to avoid any heat isues even though you wont get much from a spot welder. Now, I have done this and it is a cheaper way, you can get the panel lined up and drill a small hole and use small sheet metal screws on the flanged area. When you weld up the seam and start the process I would not go beyond 1 inch at a time and skip all over the place to avoid warpage from heat and just remove the screws along the way and weld up the holes. Use LOTS of cheapo vice grips on the lowers of the quarters to hold everything in place.
On the bottoms clean the entire area up that you are welding to with a grinder and about every inch and a half drill the hole and line up the panel and use vice grips to hold the area where you are welding. Kind of like a spot weld if you will, but just repeat this process over and over until you have welded in all the holes and just grind away to remove extra weld. Believe it or not you dont want this thing air tight on the bottom as you do need some breathing for metal sweat in the different temps weather wise. If you dont like that a light bead of clear tub caulk will seal up your quarter.

A note of concern about that flange you are making for the top of the quarter. When you are welding it up try to avoid any real hard pushing to avoid any ripples or distortion as as you weld the distortions will remain and when its welded up it will be a pain to get the flaw out and in some cases you may not be able to without using lots of torch time and sponges in ice water to shrink the metal. With that flange you are making it will make the metal twice as thick and twice as hard to correct issues. Be firm but gentle and consitency throughout and your result will be good. Lots of luck, enjoy!!
Chas.