1985 Westy (Bostig conversion, manual trans (converted))

Uploaded two pictures which you can see at this link:

http://imgur.com/cICZ1uR,iQmOCJq

I am replacing the window because it broke while I was driving.  When I got
the window out, I was kind of surprised to see rust there.

Question 1:  how does water get there in the first place (out of both
curiosity and the desire to understand what needs to be done to prevent
recurrence)?

Question 2: Does this mean I need to replace the seal?

I was hoping to avoid that expense and time, but obviously fixing something
like this would be a lot more expensive and time consuming if it went any
further.

Also:

Bentley section 64 shows, for model years 1986 or later, precise dimensions
for a bead of adhesive to be placed on the outside of the van.  They
indicate that this exact amount is used so that minimal gets to the
inside.  I'm guessing this means that the adhesive gets dragged in by the
seal as the window is placed.  Then you're supposed to use a solvent to
clean off any on the inside.

Question 3:  Should I use an adhesive on my 1985?

Question 4:  Is this the right adhesive:

http://www.oreillyauto.com/site/c/detail/MMM0/08008/N0399.oap

It's called "3M - Super Weatherstrip Adhesive"

Question 5:  Would there be any advantage to/problem with applying adhesive
after the installation?  Just using trim prybars to pull the rubber back,
and running a line of adhesive in there, is what I mean.  On either or both
the inside and outside.

Thanks in advance, everyone.

mike