saw a '67 FB with a 09 5.4 S/C and the 6 speed, the IRS, everything in it(literally the inside looked just like an 09 shelby)... he started with the K member and worked his way back, he narrowed the dash to fit, even the headliner and upper console was out of the 09,
option 1
you'll need to narrow the shock towers to fit the coyote, and widen the trans tunnel to fit the trans, you can use everything, but it requires heavy modifications to the body.
basically start with the K Member and narrowed(but reinforced) shock towers, get your
suspension on the front and work your way back. that way your steering will be easier to set up, use everything from the 15/16 on the front, you'll have to modify or build a trans crossmember... then work on the 4 link rear, definitely get subframe connectors. then all youll have to do is get the drive shaft shortened and youre right as rain.
option 2
go with a MII style
suspension/steering, eliminate shock towers all together, reinforce frame to firewall, get the right motor mounts and viola, the coyote will drop right in. then you still have to widen the trans tunnel, and implement the 4 link which has been done 1000000 times.
keep in mind the newer mustangs still use the shock tower setup but the dimensions are different, you CAN use the AJE set up, and use SN95
suspension and steering. but i dont think AJE has it set up for the late model yet. its all personal preference, im between MII and the AJE set up right now myself.