Engine Break in while in vehicle.

I'm breaking in a Ford modular 5.4 supercharged in a Ford Lightning. How should I go about this break in to apply load? Should I also be running boost, back the boost down or what I normally would be running?

You're going to get a lot of differing opinions on this though I'll say the most important thing (in my mind) about engine 'break-in' is really the fact that it isn't a break-in at all. My entire philosophy behind initial run-in is that I want to have as much time as possible to catch any mistakes so I'm listening to the engine much closer, running all the way through my rev ranges and load ranges much more slowly and sitting on them a little longer to try and catch anything etc. I do NOT think that a properly built, balanced, and toleranced engine will require anything more than initial firing, warm up for X minutes, drain fluids to punt any assembly crap out and initial inspection for glittery bits, refill, drive and after 500 miles check fluids again.

This is my own personal experience and I'll admit that the majority of my automotive life revolves around rotaries so if anyone thinks I'm out to lunch and has some info/proof/experience to the contrary I'm all ears. I've also had success on all my bikes using this method.

Pretty much the same thing, maybe with another oil and filter (I always change filters and oil together) after the first hundred miles, or so.

Start of easy and let things bed in as you work the car more until around the 500 mile mark it is at full load. You may be able to reduce that period significantly, though, depending on components and how well it was put together.