BBK makes several versions of "shorties". One is an equal length model for the 3V, 4.6 in a Mustang. Its hard to go by what the pictures look like to know if they fit. BBK hasn't been able to determine if they do fit. Thier suggestion was to order(ha-ha) and try the fitment and to inform them if it does. As long as they aren't damaged in any way, they could be returned.
The one nice feature is that the cats in the down pipes can be used as a direct bolt-on for your system. If you look at the installation PDF, you'll find the steering shaft has to be removed and the motor mounts disconnected to lift each side of the motor to install them.
I agree that long tubes will offer more performance, especially at higher RPM, but the difference between the two as far as HP gains is only 5-15 HP. Significant gains are really to be had if some motor work is done. Ex: ported heads, cams and intake set-up(manifold and TB).
In trying to figure out what to do, I've been comparing my '06 Mustang GT engine bay to the Trac and the Trac has a bit(not much) more room, so it may be possible. Long tubes would require aftermarket cats, O2 sensor extention wiring and some custom fabrication of an exhaust system to make it all work. Remember, there is only so much room under the truck. The Mustang runs its exhaust down along the driveshaft tunnel, ours is routed to one side due to the gas tank being on the passenger side.
I plan on doing all of this during this winter season(motor/headers & exhaust) $$ permitting! The motor work is not a big deal, but the Ford racing intake may interfere with the hood and the fitment of the shorties is a longshot, but necessary to make it work. I, and all of you, will just have to wait for me to see. Unless someone tries it first, keep us in the loop. Bob