I wanted to spice up my '97 F150 XLT 4x4 4.6l a bit so I put a 3" exhaust with a Flowmaster muffler; upgraded the wheels and tires (They are 1" larger in diameter) and programmed the Superchips to "Performance". It looks and sounds like a million bucks, and she ran like a raped ape for a few months then developed a bad case of the pings and in general is just doggin' it.

This is one well cared for truck; always ahead of the maintenance schedule (by dealer).

Now, any idea why it would perform so well out at first and slowly peter out?

 

I would first suspect EGR failure - or impending failure first.
Next, I would consider a clogging fuel filter.

(Notive I didn't say EGR "valve." The Triton EGR system has a bad habit of plugging up the passages in the intake plenum, or of the DPFE sensor going bad.)

 

I would also try cleaning the MAF sensor.

 

Try putting the stock program back in and see if some of your symptoms go away. If it does the tuner may be the problem and not the truck.