Try this,
After removing the window, and sanding, and wire wheeling the rust, use
a product called metal prep, by Dupont.
It is an acid etch / cleaner for the metal.

Let dry, and apply a coat of Vari Prime, acid etch zinc chromate
primer.( also by Dupont )  Skuff this down with 320, and
apply a good surface filler / primer,         (Ultra fill, by Sherwin
Williams is excellent) sand this down with 320, and paint.

When you re-install the window rubber moulding, apply a bead off black
silicone inside the moulding channel.
It will keep the H2O from getting back inside the moulding, and rusting
the metal again.

Good Luck,

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Terry 85 GL