The Whipple Tune for the Raptor has no issues, PERIOD!
It's been proven time and time again.
It's always something wrong with the install or too radical with the exhaust and is outside the perimeters of the Whipple Tune.
I am confident that Buster32 will sort it out with Whipples help!
I have a video up on the Whipple vs Roush thread, you can see the AF and the short fuel trims.
Just keep in mind that I'm running Whipple's 63 lbs. injector Tune for stock exhaust.
The AF is steady at 14 at idle and peak rpm it's at 11 to 11.5
I know the Mustangs had issues with Tunes in the beginning, until Ford came out with the GT500 Tune unencrypted.
Now everyone has used this model, and after years of tinkering around with this base model most Tunes out their are solid for the Mustangs.
Many Tuners are trying to use the same OUT DATED files for are Raptors and many have come up short.
The Raptor's PCM have new and more wide band parameters and still growing with every year since 2010 1/2 and the old GT500 files are just not compatible for the most part.
This is also the main reason for turning off the O2s and safeties, this way these Tunes can get by with out throwing every code in the book.