Assuming that it's similar to the unit I have sitting in front of me (Directed 4X03):
First of all: "All stop" until you have obtained a wiring diagram of your car's electrical system, have reviewed it, and understand it. This will answer most of your questions- such as the question in #1.
Second: the hood switch is required if you want the system to stop the engine if the hood is opened. Otherwise, ground that wire (assuming it's a negative input as most pinswitches normally are grounded)
Third: This is where that wiring diagram comes into play.
Fourth: again with the diagram. "Second ignition output" on my diagram is a pink wire with white stripe. Instructions specifically state that if it's not needed, don't use it.
Fifth: "Satellite harness". On my diagram it's 4 wires - Blue, Orange, Purple, Pink:
Blue: (-) status output
Orange: (-) accessory output
Purple: (-) starter output
Pink: (-) ignition outputs.
Good practice and electrical experience in various fields (including car audio/security a long time ago) tells me these all should be used to drive RELAYS, not interfacing directly to vehicle systems. Why do I know this? They're all outputs, small-gauge wire, and negative. This often means it's designed to go to a relay (or at the very least, it's a darn good idea, as it takes the potential for damage to smaller/cheaper components- relays- instead of frying the system brain).
Now you mention it, though- I don't see anything in my documentation about what these are designed for use as. I think it's there as a way to control functions via the RS system. It bears looking into, I will follow up and let you know what I come up with. Right off the bat, I can see this:
Blue: (-) status output - (Trigger my strobes so I can tell when the vehicle is under remote start. Parking lights would work too)
Orange: (-) accessory output - (Another "Accessory" system on the car? Would have to be separate from the vehicles main accessory systems (ie "hot when run"))
Purple: (-) starter output (really, I have nothing. Damn good question!)
Pink: (-) ignition outputs (see above. Gonna have to think on this one)
Sixth: Door locks: Identify the type of door locks you have, first. Rest at Positive, Rest at Ground, what? At any rate, I would recommend using the door lock outputs to run RELAYS which then interface with the door locks. Same reason as before: if you have a bit of extra draw through the system you want to replace a $8 relay, not a $100 RS brain. This honestly isn't such an issue if you get a new car every few years, but if you're like me and keep them a while, eventually the door lock motors will start to bind- drawing more current- and this could fry the traces inside the RS or Alarm unit brain. Of course, regular service helps, but who pulls their door panels apart and lubricates the door locks?
ABOVE ALL: If you are planning on just going with what someone on the internet says ("cut this wire, splice it in, and you're fine"), then STOP. Take the equipment to a reputable installer and let them do it. Yes it will cost money. But it will also SAVE you potentially thousands. ECUs and BCUs are NOT cheap. Your car is new enough that you probably have both.
No offense at all meant in this. You seem like you've not done this before. I am not trying to offend you when I say you have jumped in the deep end of the pool, and there be sharks there....
I and others on this board will help you any way we can- but when it comes down to it, if you fry your ECU we'll all feel real bad for you- but it's *YOUR FAULT*. Yes, there may even be laughter, I've been the subject of it as well. ;)
Another thing: if you're planning on using a test light, or logic probe for this install- don't. Use a quality DMM (and I'm not looking at Harbor Freight here). Test lights (except for very specific units, made for the use) are by their nature capable of frying the delicate circuits in the car's control units. I'm talking from personal experience here, as a professional installer... in 1991! The situation hasn't gotten any less complicated since then.