you could weld the spot welds through your existing holes from the front side if you wanted to still go that route. smooth both sides of the flanges area first, then hammer and dolly the flange flat, then slip the new step flanged panel in behind and screw it down through some of the existing holes, using flat washers under the tek screws to help distribute the forces and keep the flange flat.
just some ideas.
if you have a big enough air compressor to allow sand blasting with a small blaster they work well to clean up the rusty areas behind the removed panels. use a flap disc or a strip disc fist to remove as much as possible fist and then the sandblast time is way less. as well as the clean up time after in the shop (I do mine outside if possible).
one of these types can also be used with a hose into a bucket of sand
https://www.lematec-tools.com/lemate...e-tool-as118-2
I also have one of this style with it's own bucket
https://articulo.mercadolibre.com.mx...xoCvoIQAvD_BwE