Sorry, but you will make absolutely no power n/a with the mmr upper, it was intended for boost. All the runners are different lenghts and shapes ( I know I have one sitting next to me). You cant run adapters on that either, they dont just space the intake higher, its to mate a 4.6 (more narrow) intake to a 5.4 (wider) block. If you get a decent intake, like a sullivan, you can make way more top end power! I know they are a bitch to find but its worth the effort to look. I would not look into a boss 260/290 intake unless you are going to run 99-04 4.6 C heads, navi heads are 10mm larger around the entire port. You will get bad turbulence in the intake runner, it will make good torque, but up top it will kill power with the quickness. If your feeling creative I would go with the boss 302 coyote intake and do some port and epoxy work to it, to line the runners up better, they already have around an 8" runner I believe.
If you run this upper manifold on a stock navi engine you might crack 330-340 at the tires. There have been other people barely crack 300 to the tires with a cobra intake with adapters. To make any decent power, you need CUSTOM cams, not the crap comp's (they are designed for a 4.6), longtubes, exhaust port work (intake side is good how it is), A GOOD intake manifold, and lots more compression. Run 4.6 flat top pistons with 5.4 rods to get the extra .100 compression distance. This will bump you over 12.5-1 comp, which these things love. They already have mahle flat tops in the navi engines (the same as the 2000 cobra R), so if your doing boost down the road, these would work well with a good rod to support the power. The bad thing is they sit in the hole around .120 which kills your compression to around 9.5-1.
supposedly flowtech longtubes will work if you drop the engine a bit and bend some of the primaries. In my book that is totally worth it. Run a full 3" exhaust as well.
In the end its your car and you can do with it as you please lol! Just sharing all the knowledge I have on a 5.4 4v swap. IF you do it right with cams, compression, and correct port work and a good intake manifold, you should crack 400rwhp no problem.
