I've looked into this a few times. I can't remember why, but there was an issue throwing a lightning computer in place of my 5.4/auto F250 4x4's. I can't remember if it was GEM or 4wd issues. Which is why I went with the tuner I have.

The heads and all should work, as long as you stay with the 2v. 4v heads would be a problem with the lower manifold, as I haven't found 5.4l 4v motors that were supercharged. 3v heads are a pain because of the vvt.

I recall the pistons being hypertuaric (sp?), so you really need to make sure it gets plenty of fuel. Starving it down wouldn't be good. Then there was the issue of the bottom end. The lightning had a forged bottom end and the N/A motors didn't. You kind of need to keep that in mind as you shoot for power and reliability.

Which is why my conversion is at a stand still. I want to fix up the bottom end first, then slap one of the bigger kenne bells on it. Which you may want to look at, KB had an upgrade option for the Eaton drives. I can't remember if it was the 1.8L, 2.4 or 3.2L blower, but it was an upgrade and relatively cheap.