There might be a recall on this ...
Exhaust & Emissions: ENGINE AND ENGINE COOLING:EXHAUST SYSTEM:EMISSION CONTROL:GAS RECIRCULATION VALVE (EGR VALVE)
Service Bulletin Number: 7219
NHTSA Number: 10023855
Model Years Affected: 2003, 2004, 2005, 2006, 2007
Date of Bulletin: 02/2008
Bulletin Summary: 6.0L--MIL ON--P0401, P0402, P0404, P1335--LACK OF POWER OR SURGE WITH SOME 2003-2007 F-SUPER DUTY, 2003-2005 EXCURSION AND 2004-2008 E-SERIES VEHICLES.
This is under your 2006 Super Duty Common problems and Recalls on www.repairpal.com
the egr is centered on the top, front of the engine. it has an electrical connector attached. it can cost $304.00 for a new one at autozone, "OR" you can try cleaning it and spend about $1.99 for a cheap "value" brand can of carb cleaner, a used tooth brush and a steel brush. the egr gets sooted up like crazy and so do the ports inside the intake. the intake needs to be vacuumed out.
i just answered your question with thw $1.99 cheap carb cleaner. i forgot to say that i just did this. my "service engine" light came on and I pulled 4 error codes. all codes cleared after i spent the time (not money) to properly clean the egr and the intake cavity ports. about an hour labor and $1.99 leaves me with plenty of beer money!!!