So I noticed a little cancer this morning. Any suggestions short of calling the glass company to pull and replace the seal and repair rust while its out?

 

Which window?

Probly got to pull the glass to fix it right

 

Looks like your Alpine window and from the looks of it you need to act fast.

I'll give you the quick version.

Remove the interior panels that are behind the windows.

Using a plastic panel tool, pry up the INNER rubber moulding on the outside of the window rubber. Pull out completely.

Use the plastic tool to work out a corner of the window rubber and window.

Move to the outside and pull the assembly out.

Use a scotch brite pad on a rotary grinder and remove any loose rust, but not to much because you will create holes.

Use a rust reformer product to convert the rust to a paintable service.

If you created any holes, I use metal tape to back the holes and patch the holes and grind marks with thin skin of bondo. Sand

Get a can out touch up and clear from automotivetouchup.com.

Paint per instructions.

Once ready, use a thin film if clear silicone caulking in the valley of the rubber gasket(with middle insert still out). Work window back into place.

To put the insert back in, line up corners, center points, and seam to make sure it is distributed in place evenly. Push back in. Do not start at end end and work your way around, you will end up with extra.

And just in case you are new to this kind of work, drink beer.

Good luck