Right. The 5.4 deck height is taller, which mounts the heads higher and further apart.
The aftermarket has the DOHC engines covered by Sullivan, however, the 4.6 and SOHC engines (At this point) require custom intakes from Hogan or building your own.
DOHC: Sullivan Performance cast single plane intakes... $600, but requires their rails and if you run a single Cobra or Lightning TB, you need the 90 degree adapter. A 4 blade TBI type TB is available as well, for use N/A or with a carb hat for blowers and turbos. Adapters are at an additional cost.
http://www.sullivanperformance.com/index.htm (DOHC and soon to have M-112 castings available as well).
I AM in contact with a few manufacturers and they ARE working on them, but to my knowledge, not soon.
Hogans: CUSTOM intakes. ($1200-3200)
http://www.hogansracingmanifolds.com/
I know Sullivans stuff well, however, just got docs on the Hogans. Go over the site to see what they can build. QUALITY does not come cheap. These are sheet metal, NOT castings.