Pat, Looks like a good start. Carl's suggestion on using self tapping screws is a good thing.
I think that any hinge pillar twist caused by the door over-extending will be a problem, as cutting the outer cowl away should relieve the pull on it. Your crease doesn't look like it would have caused any permanent displacement of the hing pillar.
My suggestion on placement of the outer cowl is to measure, measure, measure, and measure again.Be sure the door fits before committing to welding that piece in. Measure across the opening at intervals below the belt line, comparing those opening measurements to the door width at the corresponding intervals.
You're planning on using the whole outer panel, which I think is a good plan. I only used the lower section of the outer panel, because the upper part was still in decent shape.
