Here's my 2cents worth.
The 4.6, 5.4 and 6.8 are all modular. Ie: Built with many of the same parts. You can swap them. Anything is possible when it comes down to time and money. As a guy speaking from the challenge of putting the 6.8L V-10 into my '93 with twin turbo's that has been almost 2 years in the making, I would say this... Take the stock 4.6 and add a Vortech. Simplest install. Makes decent power. Easy to tune.
Drive around with your 350 to 400 rwhp until the stock block dies and then have the block professionally built up for big hp/big boost. For around $5000 all said and done with tune, you have a nice streetable car that will beat most on the road.
I have seen 4.6's make 1000hp. I have seen 5.4's make 300hp. So my opinion is keep it reasonable and you will be able to enjoy the car out on the road instead of sitting in the garage like mine does. Apply the KISS principle to enjoy more trouble free miles.