I currently have a Trickflow R Series intake on it. However, many have told me I'm leaving horsepower on the table and have since purchased, but not installed, a Trickflow Box R intake.
I'm currently running a Terminator X and am happy with it. I went back and forth about different valve covers, but am happy with the flat black non descript ones which came on the engine from Ford.
I have a stock height fiberglass hood with no underside cross bracing. I wanted to maintain the OEM look and the no underside cross bracing frees up some height. While the Box R is approximately one inch taller than the R-Series, I'm currently running a spacer and suspect the height will be nearly the same without the spacer on the Box R. If the Box R does rub the underside of the hood, I plan to have it machined down a bit.
Good luck and check out my progress thread below. It has a lot more info.