I did the same I blocked off the exhaust side and put a k&n on the intake side.The flapper is removed car has been this way for a while. I would say better mpg and better highway response when you get on it. Thanks for checking on the chip I am actually going to turbo the car after next year. I am getting a 603 injector pump and going to put a inter cooler in the set up.
http://www.schumanautomotive.com/forums/index.php here is a good link to another site with a bunch of diesel guys.