Hey Eric.  I've got the following setup in my van.

Subwoofer - Infinity Basslink II - 200 Watt under driver side jump seat.
Remote volume knob on bottom of dash.
Alpine 9803 - 45w X 4 RMS head unit
JL Audio e4300, 4ch (360W RMSX4) Amplifier under passenger seat
Replacement Rear Speakers (Kenwood 5.25") had to enlarge holes for speakers
but they fit nicely
Replacement Front Speakers (MB Quart DSC 6" Bass Driver, 1" High)  had to
enlarge holes for speaker.  They are very flat and would not interfere with
window cranks.  But I have motorized windows so my tweeter would likely
interfere with a window crank. But it can be positioned to avoid that.
Here's a pic of the driver side door with driver and tweeter in place.
http://www.weidefamily.net/vanagon/HTML/07/02/images/04.jpg

The 6" speakers in front give a very good tone and the subwoofer fills in
the lower end very nicely.
Good luck with your project.
Brent

--
Brent Weide
Portland, Oregon
www.weidefamily.net/vanagon/

--
Brent Weide
Portland, Oregon
www.weidefamily.net/vanagon/