There is no limit on power just like the 03-04 Cobra heads.
The bolt pattern on the heads are different and you will require a custom intake. If you have a 5.4 with Cobra R heads then a Cobra R lower will bolt up.
There are no intakes that will fit on a 4.6 with Cobra R heads.
You will also require different intake lash adjusters. The 03-04s cant be used.
You will also have to modify your exhaust manifold flanges due to a different bolt patten. IIRC.