I had this problem on a fiesta mk5 which is the same basic shape as the mk3 frst.there's three bolts on the back of the box where it mounts to the cradle.their studs on the escort(poking out) and caphead bolts on the fiesta box.I tried doing all the thigs you said to no avail until I noticed this.
Pulled the box off,swapped the bits round and it flew back in,everything lined up spot on.