I have a 2003 Ford F150 FX4 with 5.4. I have been getting about 9mpg lately and can seem to figure it out. I just put new plugs and fuel filter in and it was straight piped from cat back but now have a flowmaster 40 on it single in single out. I am beginning to believe I have a vaccum leak due to the poor fuel mileage, alittle funny idle, and my 4x4 does not engage on ground but when it in air it works fine which don't make sense. Also when I'm sitting in park and idle and hit brake it kinda shutters but not real noticeable so I'm thinking either vaccum line or brake booster. Also once that is fixed how many of you run a programmer on your truck. I have been thinking about it just to gain a few more mpg and it would pay off for itself after a year pry. Which programmer are all you running..I'm thinking a SCT

 

This is only a 'discussion' at this point for your consideration because you have nothing to go on but noteable low fuel mileage.
First thing is the exhaust changes have not been helpful for a truck application.
Likely have lost some low end torque which makes you to put your foot down a little more. That uses more fuel.
Next, it's winter time therefore the truck will noteably use more fuel.
Using a tuner can cause you to override any gains by using whatever extra power you might get, so the results tend to cancel out on average for mileage gains for the cost of a tuner. (This becomes a point of self honesty for what you do with the foot).
Next, do a scan for any pending codes that may point to an issue.
Then have a look at the long term and short term fuel trim tables to see if they are out of line with the average expected.
Last, if your CEL lamp is not on at this point, the computer does not see a vacuum leak unless the trim tables as talked about just above, have moved out of limits setting codes to indicate a leak.
.
One thing to check is the operating temperture of the cooling system.
If to far under about 195 degrees fuel mileage can be affected without any fault indications or CEL dsplayed.
Your trying to second guess an engineered system without any background understanding and assuming you can make change on the outside of the system to improve it which most of the time it does not work to that extent. There are to many vairables that affect the outcome.
The PCM runs on a program you cannot greatly change, from inputs from sensors off the engine.
The program runs on tables that have high and low limits so are self adjusting in reactions to the outside sensor feedback signals. This is why outside mods can make things worse.
Moveing around in a 6000 lb + truck and expecting fuel mileage is almost a mis-nomer
Not saying you may not have some issues that could be cleaned up but you need to look for them first before just assuming changes will be the fix to your concerns.
Remember, this is just a discussion at this point because I talked about things you might not have wanted to hear or agree with but it's good to hear them as part of learning and reference.
Good luck.

 

Did you replace your coil boots and springs?

Also, did you inspect the coils for damage?

Here is what I am talking about.



I suspect you have a miss.

The exhaust mods didn't help, stock is best on these trucks.