Keith, the Ford Taurus and Lincoln Mark VIII fans are dual speed fans with a single fan. There is a ton of information on the 'net as well as Hybridz/LS1tech about this (and the Lincoln Mark VIII) fan.
Exactly.
Mike, your car really should not be overheating. I have a very similar setup: LS1/4L60E, cone filter protrudes from the side into the radiator area, and the trans cooler hangs down a little in front of the radiator.
I know you said you and your buddy made sure you tested the system for air, but it could not hurt to check again. Have you checked the thermostat? Is it opening? It sounds like your fan is operating on high the entire time you are driving (both around town and at highway speeds).
Just had a thought.....what about your lower radiator hose? I had a helluva time trying to source mine so I cobbled together an ugly frankenstein hose. Recently, got tired of looking at it and decided to replace it. Well, all of my replacements wound up severely kinking after one heating cycle. I went a slightly different route and used two 90ish elbows with a section of aluminum pipe. What is the condition of your lower hose?