I get the same thing with my setup.
2010 FX4 5.4L V-8
Magnaflow Catback SI/SO
K&N CAI
It sounds nice and deep when at a slow parking lot cruise but when I hammer it and at some RPM's I get some drone. I was thinking of pulling my CAI and going stock to see if there was a difference.
I talked to Magnaflow and they said to add a resonator to reduce the drone.

 

That is the drone I was talking aobut with the 5.4L that I didn't like. All those crazy looking baffles really do something. I ended up just running a K&N filter, couldn't stand the drone from the intakes.

EDIT: Had the Magnaflow on my 5.4L as well, it droned on the highway but was manageable.

 

I only have drone since I added the K&N, with just Magnaflow it was fine even when I hammer it

 

did you remove spare tire to get the exhaust to fit fine?

 

No the spare tire was not removed

 

Hey Shick, i have the same setup, K&N CAI with Magnaflow SI/DO behind rear passenger wheel like the harley, the drone is only from the CAI. It has the same drone as the GOTTS mod(wich i put back)

I will post pics

 

Thats the same setup i want if you can i want to hear how it sounds and pics will be awesome. Finally i found someone with that setup

 

I have the same setup on my 5.0 2011 and when i push it there is a vibration in the cab .
but it s more responsive.

 

I painted the tips cause i don't like chrome







Trying to get a video clip

 

I like the look of the painted tips! Did you use a special paint? Also what size are your tires? Are they a lot noisier than stock? I'm looking at going with that same set up.