i have the same car as you and have had a few setups with anew hu
from the pics it looks like you have the keyless entry AND the alarm system, is this true?
i only have the keyless, which is built into the cd player, the extra box is the alarm portion, and i dont know offhand how to wire that

i need to pull mine and add a wire in anyhow so if you need more pics or anything let me know, i can do it tomorrow
good luck, sounds like you will do fine

i have my stock stereo in place, and an alpine hu down in the lower pocjet, this allows me to keep a stock look, have a permanent clock, and also reduces glare on the faceplate, so you should think about that as well

i will write up the wiring config later if you cant get it figured out, its basically what you said though, power, acc, ground, maybe one more
i know on mine i need to add one more wire so it dims when my lights are on