[rossisnow]

Sounds EGR related. The EGR should be off at startup, otherwise it can make for rough idle. Check your vacuum switches. Works better when warm which is probably why it "cleared up". EGR flood can cause incomplete burning of the fuel leading to bad mileage. The intent of EGR is to cool the combustion chamber therby reducing the formation of NOx and CO2. Might be why your running cool.

Also, what he said.