Keep in mind that I am absolutely no expert in body repair, I'm sure allot
of others can chime in as to how to do this.

It's really hard to tell how far the rust has penetrated under those window
seals from the photos.  If the lip is all rusted out I would assume that
would need to be fixed by putting new metal in there. I have no idea how
that is done for windows. If it is all just surface rust you can probably
just pull the rubber out, take out the window and sand/grind and treat the
rust.  Putting the windows back in can be a pain (I've done 1 before) but it
can be done and also I believe a glass place can put them back relatively
inexpensively.

As for the rust coming back, 10 years might be a little optimistic but then
again this is the first time I've used that POR-15 stuff. My rust came back
after about 5 years. This is also the first time I took out the camping gear
to get behind the rust for the drivers side seam though. My van also used to
sit outside 24/7 under a bunch of trees. It's now garage kept as of this
spring.

Hmmmm. Tools. Well if you were going to replace metal I have no idea what
you'd need as I've never welded and don't plan on it. For fixing rust though
I use a wire brush, a wire brush for the drill, a Dremel grinder, chisels,
hammer, belt sander, orbital sander, sandpaper, and a good respirator. I use
fiberglass mat and resin for holes and finish with Bondo Glass (hard to work
with but stronger than regular Bondo) and spot glaze. The fiberglass resin
is really strong, so strong that it was a real pain to get the previous work
off the van for this time around since I was fixing the seam rust from
behind.  It all had to be chiseled off in pieces.

$400 a window? Is fixing rust that expensive these days or were they going
to cut your old window frames out and weld new ones in?

Bryan