I dont see where a 5.4 costs more to build than a 4.6. A 4.6 BB block costs about 4 times as much as a 5.4 block. The heads and cams are the same. 5.4 forged cranks are dirt cheap and the pisons/rods cost the same. You can use adaptor plates for the intake. Headers are a issue though. I would build my own shorty headers that pointed forwards.
A 5.4 bolts right into a mustang with the K-member shimmed down about 3/4". I never put a 5.4 in a mustang myself and Im sure there is other issues. I did build a 5.4 4V turbo motor for a guy and his mustang had everything other than the AC.
That being said the next motor I build for my car will be a 4.6 BB iron block with a BIG turbo.