There are at least 10 different intake manifolds that were available for the 4.6 2 valves that I know of.
Typhoon - Professional Products (junk)
Reichard Racing
Bullitt
P-51 - Fox Lake
Logan Motorsports
Hogan Sheet Metal (must rob bank)
Edelbrock (out soon?)
Trick Flow (out soon?)
Wilson Manifolds (must rob bank)
VRI
Like SanMan mentioned most of these either eliminate the need for the upper plenum or use their own. The Typhoon is the only one that will use the stock type plenum, but after seeing a few of teh Typhoons and their terrible casting, I would never persoanlly use one even if it did show power gains. The Logan Motorsports is going on my car later this year. It is less than a grand and has proven to perform very well.
It's not necessarily how the heads and intake manifold flow independantly, it's how they flow together. Whenever you flow test a cylinder head with the intake manfold bolted to it, the flow numbers will always be less than when the head is flowed by itself. It's all about optimizing them to work together.