Richard, Attempting to mig weld rust holes may not be a good idea.
I'd take the roof down to bare metal. At the rusted area use a 25 grit sanding disk which will prep the area for the filler. After sanding, slightly dimple all the holes with a clean center punch and apply a thin layer of premium light weight filler. Sand and fill, sand and fill, sand and fill, till it's smooth. Prime and paint.
When you got the outside done, seal the inside with por 15 to keep any moisture from attacking the area from the inside.
Who knows, you may bring the car east some day.
That's what I would do.
If you decide to go the mig route, keep in mind that it doesn't take much heat to warp a large area like a roof. Enjoy.
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