I too have a 2006 SuperDuty with the 6.0 and it just needs to be maintained.
Oil filter is on top of the engine the larger of the 2 . The smaller one is your secondary fuel filter.
Look up 6.0 coffee table book and you can download that and get a real good education on the engine. There are several books get the 2003 and the 2005 up ones.
Like kinnisoj stated get yourself some gauges for the truck. I have the ScanGaugeII for my truck, they cost $ 160.00 at Auto Zone and it is a on the shelf item. This plugs into your OBDII port under the dash and you leave it plugged in all the time. This will allow you to monitor the engine as you drive and can also be used to trouble shoot it in the case you have a problem. Its also a code reader so for the money there is nothing that beats the ScanGaugeII.
I use it to monitor the oil and engine coolant temps. Also the FICM and alternator at all times. There are 24 different things you can program it to monitor anytime you wish to see whatever point.
You don't need studs or a egr delete or anything else if you leave it alone and don't tune it. What you do need to do is maintain it !!
Oil: should be a synthetic 5W/40 and ONLY use Motorcraft filters. Change it every 5,000 miles.
Fuel filters: again Motorcraft ONLY. change them every 10,000 miles
Coolant: Ford Gold has been a problem for the 6.0 when it is ran too long. The coolant has silicates that can become a problem because of the high heat it endures from the egr cooler over time.
Solution for this is: Flush out the cooling system with Cascade liquid dishwasher soap and flush out good with water then distilled water. Replace the coolant with Cat EC1 coolant. You should then invest $160.00 into a coolant filter that is well worth the money to ensure a clean cooling system.
The cooling system can have debris in it and if it gets into the oil cooler it will plug it up. If this happens it sets off a chain of events that is what gave the 6.0 it's negative reputation.
Basically the oil is cooled from the cooling system with a oil cooler that is under the intake manifold. After the coolant goes through the oil cooler it goes through the egr cooler then back to the radiator. If the oil cooler plugs up the flow of coolant is reduced to a point that it can no longer keep the egr cooler at a safe temp. If this happens the egr cooler will reach temperatures where it will crack and leak coolant into the intake manifold. From there it can go into the combustion chamber then causing extremely high cylinder pressures and blowing the head gaskets.
So you want to make sure you keep the cooling system on your truck clean. A ELC type coolant is what International uses in all of their engines. Ford on the other hand wants to sell their product for the Powerstroke of coarse. In reality the Ford Gold is fine to use as long as it is changed every 25,000 miles. I myself do the same 25,000 miles with the ELC coolant so run whichever you choose, but most of us have gone with the ELC like the Cat EC1 coolant. Mainly because it is silicate free and will go much longer without changing then the Ford Gold would ever last.
Ok so flush the cooling system and install a coolant filter. There are several different brands of coolant filters including some newer full flow models that filter much faster then the most common ones like my (Sinister) model.
So changing the oil and filters also change your fuel filters and deal with the cooling system. By doing these things and keeping on a proper schedule you will eliminate the problems that you can have with a 6.0 engine. I hope I didn't throw out too much at you but that is the basic facts on a 6.0 liter PowerStroke.
I'm not done yet, once you get that ScanGauge program in the oil and coolant PID's and take the truck for a 30 minute drive on the highway at 65 mph on level ground. What you want to do here is determine the health of your oil cooler now.
What you should see with a good oil cooler is: ECT temps around 195* and your EOT temps 5*-9* degrees above the ECT temps. (ECT=engine coolant temps) and the other abrv. is : ( EOT=engine oil temps) If you are in this range your engine is good to go just do the coolant change along with oil and fuel filter maintenance.
There are other points to look at like FICM should be at 48 volts all the time period.
There is also a fuel pressure regulator upgrade worth the time and money. $ 40.00 and about 30 minutes to install the newer upgraded spring. This will raise the fuel pressure back to 60 psi, the original spring was too soft and it looses spring pressure therefore dropping the fuel pressure.
I hope I didn't overload you here, there are some things that should be done with the 6.0 to make it reliable. These are what it needs to have a reliable engine. Head studs or egr delete is not must do items unless you are going to tune the engine.I have 82,000 miles on my truck and it runs like a Swiss Watch. The 6.0 will leave the 7.3 in the dust in every category. It has a much higher degree of engineering then the 7.3 could ever wish for. But with this comes more critical maintenance schedules that need to be kept up on.
You have a great engine with loads of power and it can be tuned even with the factory tty head bolts you just need to know which tune is right for you conditions. Congrats on the truck odds are it will be the best one you ever owned.
2006 F250 LARIAT CCSB 4X4
ARP Studs, O-Ringed Heads
X4 PHP 65 HP Custom Tow Tune
Atlas40 or Atlas80 Ficm Tune
CAT EC-1 Coolant, IPR Coolant filter
BPD Waterpump, BPD way of thinking
Fass-125 to a Adjustable Pressure Reg.
Turbo-back SS 4" pipe, Corsa Muffler -7" Tip
6.4 starter, DC Power 270 amp alt
Die Hard Platinum AGM all 2/0 Cables
Fabtech Radius Arms
7" lift w: Icon Progressive Coil Springs
2008 up Carli/Deaver rear springs
All riding on some Fatty-Daddy 38/15.50/18 Toyo's