I had such a conversion done on my 87.  You have to remove the tunnel 
inorder to make the opening for the top.  The guy who did mine cut the 
tunnel off at its output from the rear deck.  He then put a cool 
carpeted box around it with louvered vents.  Its kind of like a jet 
engine blowing towards the front of the vehicle but for me, AC is not 
something I ever use so I don't care so much.  If I could borrow a 
digital camera I could include lots of details about doing the top.

The problem for me is what do you do about the headliner in the front 
that has the other end of the cut AC tunnel.  The guy simply covered the 
end with carpet.  I am in the process of cutting out all of the front AC 
vents and making map pockets over the driver/passengers head.

Hope this helps....
When you get the top from that other van make sure you grab everything 
including the plywood bottom pieces.

Chet
-- 
Chet Douglas - CRD Consulting - Peripheral FW,SW,and Drivers
(541) 754 - 1817