Well... I'm crossing that bridge now (but slowly).

Stuff like headlights, turn signals, brake lights, interior lighting, door jam switches, horn, etc, shouldn't be tied in with your engine harness (like motoxlifer said). The main thing you'll need to do is confirm what you need for proper cluster operation & power to the engine harness (& components). If you decide to get a custom engine harness, that'll make things a lot easier (trust me, I managed to make the stock 5.3 harness work the proper way). A custom harness may seem pricey, but it's probably worth it for most people. I'm comfortable with doing my own wiring, but most people aren't.

Any more questions? If so, post up... folks are here to help.