I ran into this same problem just this week during my camper conversion.
The side sliders I got from a '87 Westy is about an inch shorter than
the ones in my '84 GL.  I didn't realize it until I had BOTH windows out of
my GL.  I had to put the same windows back in.  It gave me practice both
on changing windows and saying the Serenity Prayer.  I was also asking
WHY.

Charlie in Colorado

----------
>From:  KENWILFY@AOL.COM[SMTP:KENWILFY@AOL.COM]
Sent:   Wednesday, May 05, 1999 9:19 PM
To:     vanagon@GERRY.VANAGON.COM
Subject:        A real pane! or A tale of two windows

I have a customer's van here with a broken window in the sliding door.  It is
an '85 Vanagon GL.  The window is a sliding one and a have a couple used ones
from some Vanagons I parted out so I thought no biggie I can replace his in
no time flat.
Nope!  Here is what I ran into.  The '85 sliding window is one inch shorter
(in width) than either of the other windows that I have (one from an '84 GL
and the other is from an '82 diesel).  So the question is why?  Why would VW
make two different sliding windows only one inch different from each other?
All the other Vanagons I have here ('84 GL and 85) have the smaller window
(same as my customer's van).
Now I have to find a window that actually fits.  I'll email with the actual
dimensions tomorrow as I don't have them right now and I am sleepy.
Ken Wilford
Van-Again
John 3:16