That middle photo is the '99 Cobra 4.6 and NOT a 5.4L engine...
The two-valve will fit with minor trimming of the towers for exhaust manifold clearance and the use of special motor mounts by DVS Restorations...
Anything else 3V, 4V, 5.4L will require removal of the shock towers.
As for why to keep the shock tower, they were an original design element of the chassis and are structural. Adding a MII crossmember, while upgrading many areas, should really be reinforced for big engines and big power. Plus, that 50 year old suspension technology still works with some nicely upgraded components. You don't always have to throw the baby out with the bath water you know...
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