Welcome to ecomodder KamperBob. This is the best site on the web on the subject and you will learn alot here as I have.
On your questions, I will defer to others to maybe explain about the air flow over the top opposed to the sides of a pickup. Also, on the computational fluid dynamics, even though I have sculpted models which were scanned for CFD, I have never ran a simulation myself. There are others here also who may be able to answer your question about the CFD program.
There is some good information on the web on how to build a wind tunnel but they can get expensive. The following link is from a couple of students at Western New England College who built a water tunnel and tested a pickup truck model in it. Their resulting Cd numbers are real close to the real world in scale so decent data can be gained from a simple wind/water tunnel.
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