Looking at the last picture, the part they took out is full of rust which means fuel contamination (water/moisture in fuel). Whether a tank of water or the big discussion on here and other forums on water in the fuel that is basically blended in with the fuel therefore not triggering the WIF light.
As stated by djousma, the High Pressure Fuel Pump is AFTER the primary filter so if it grenades after the filter, some of the access fuel not used gets rerouted back to the tank and will be caught by the primary filter however it is already too late because it as already done a full loop.
The 2nd picture is hard to tell what it would look like since it is still wet from fuel. If it is dried off, my guess is that has rust on it as well.
As I stated in a separate thread, everything you need comes in a kit from Ford. Ford simplified the ordering process for fuel contamination for the dealers. The kit can be had for about $3,700 online from the discount FORD dealers and the book lists the repair at about 17 hours. You should be looking at a $5,500 repair if you bring them the parts. What they are doing is charging you for the parts SEPARATELY instead of passing the savings on to you and charging you for the kit.
Here is the kit: EC3Z-9B246-A $3,084.15 (plus core charges that you would get back).
KIT | Genuine Ford | EC3Z-9B246-A
You also need the frame mounted fuel pump and the fuel filter kit.
I believe this is the pump that is needed but you would want to verify BC3Z9A543A $905.18
INJECTION PUMP for 2014 Ford F-350 Super Duty|BC3Z-9A543-A
The filter you can get at your dealer or from an online dealer at a discount.
Regardless, taking the filter out of the equation, $3,989 for the parts needed plus labor. This is 10% above cost so true cost to dealer is about $3,590.
I remember reading from someone going through this that they took the kit part number to their dealer and they flat out told them that they will order the kit but still going to charge him for the parts individually. Considering cost is $3,600 and labor is $1,900, they are looking at $5,500. Anything above that is pure profit. I understand dealers need to make a profit on service BUT $5,000 on a day and a half job is ridiculous.