nothing wrong with cutting out the old bad places and welding in new metal. It doesn't have to be perfect in shape, but in structural strength. It is all covered by the outter parts. Make it strong. Just seal it up good so it doesn't hold water and dirt.
Under the kick plate on the door sills you can drill holes to pump in anti rust formulas and also blow out dirt. Then cover the holes with duct tape and replace the door sill plates. Easy to get to each year or so to do again.