A 2 micron fuel filter is a plus for the system, but I recommend a dual filter system, the fuel/water and final filter system before the standard filter housing.
The fuel pump is strong for this year as mentioned before, but I recommend, since it's an '06, look into 2 stroke oil for each gallon of diesel at fill up (1 oz per gallon). I've used it for over 60k and it's a positive. It doesn't add mph, but the '06 is still in the years for sulfur diesel recommendation in an Ultra Low Sulfur Diesel age, and the missing lubecity can wear the system in time. Also it quieted the engine noise some.
As for the 48RE trans, if you change the oil as recommended it will last a long time, but don't adjust the bands unless it indicates it indicates it needs it. That's from a trans man that I found has been in the business for over 35 years. He has 245K on his Dodge without an adjustment and his is a daily driver plus pulls heavy 2 to 3 times per year..
One thing to consider is adding a coolant bypass system. Not very expensive, helps keeps the coolant clean, and if your drawing from the head plug between #5 and #6 cylinder, it add more coolant movement to that portion of the engine, that is normally a low flow area compared to the rest of the head.
I also recommend an oil bypass system. Cleans the oil of smaller debris and also scrubs soot from the oil. (really improved my oil sample results) Normal oil filters are between 35 to 40 microns and a bypass filters 10% of oil every hour at 2 microns.
For the standard oil filter, I recommend the Donaldson ELF oil filter, it's rated for 17 microns, and that's way better than stock filters.